Цель занятия - понять, как получаются полуэмпирические и Ab initio вычисления молекулярных систем.
Сначала попробуем получить оптимизированную структуру порфирина.
Загрузим модуль pybel и посмотрим, какие форматы он может читать и писать:
In [1]:
import pybel
In [2]:
print pybel.informats
print pybel.outformats
{'txyz': 'Tinker XYZ format', 'text': 'Read and write raw text', 'alc': 'Alchemy format', 'CONTFF': 'MDFF format', 'castep': 'CASTEP format', 'nwo': 'NWChem output format', 'cdx': 'ChemDraw binary format', 'xml': 'General XML format', 'pwscf': 'PWscf format', 'jin': 'Jaguar input format', 'rsmi': 'Reaction SMILES format', 'xtc': 'XTC format', 'g09': 'Gaussian Output', 'pcm': 'PCModel Format', 'mopin': 'MOPAC Internal', 'dallog': 'DALTON output format', 'mopcrt': 'MOPAC Cartesian format', 't41': 'ADF TAPE41 format', 'fchk': 'Gaussian formatted checkpoint file format', 'g03': 'Gaussian Output', 'cube': 'Gaussian cube format', 'axsf': 'XCrySDen Structure Format', 'mpc': 'MOPAC Cartesian format', 'mpo': 'Molpro output format', 'mop': 'MOPAC Cartesian format', 'pos': 'POS cartesian coordinates format', 'dat': 'Generic Output file format', 'moo': 'MOPAC Output format', 'dx': 'OpenDX cube format for APBS', 'mol': 'MDL MOL format', 'inchi': 'InChI format', 'hin': 'HyperChem HIN format', 'cml': 'Chemical Markup Language', 'outmol': 'DMol3 coordinates format', 'xyz': 'XYZ cartesian coordinates format', 'lpmd': 'LPMD format', 'xsf': 'XCrySDen Structure Format', 'qcout': 'Q-Chem output format', 'output': 'Generic Output file format', 'orca': 'ORCA output format', 'mdl': 'MDL MOL format', 'exyz': 'Extended XYZ cartesian coordinates format', 'dalmol': 'DALTON input format', 'unixyz': 'UniChem XYZ format', 'pdbqt': 'AutoDock PDBQT format', 'gzmat': 'Gaussian Z-Matrix Input', 'arc': 'Accelrys/MSI Biosym/Insight II CAR format', 'pcjson': 'PubChem JSON', 'out': 'Generic Output file format', 'smy': 'SMILES format using Smiley parser', 'c09out': 'Crystal 09 output format', 'feat': 'Feature format', 'crk3d': 'Chemical Resource Kit 3D format', 'got': 'GULP format', 'mopout': 'MOPAC Output format', 'tdd': 'Thermo format', 'mmod': 'MacroModel format', 'siesta': 'SIESTA format', 'bs': 'Ball and Stick format', 'mmd': 'MacroModel format', 'box': 'Dock 3.5 Box format', 'bgf': 'MSI BGF format', 'fa': 'FASTA format', 'POSFF': 'MDFF format', 'vmol': 'ViewMol format', 'acr': 'ACR format', 'pqs': 'Parallel Quantum Solutions format', 'crk2d': 'Chemical Resource Kit diagram(2D)', 'CONFIG': 'DL-POLY CONFIG', 'pdb': 'Protein Data Bank format', 'ck': 'ChemKin format', 'c3d2': 'Chem3D Cartesian 2 format', 'aoforce': 'Turbomole AOFORCE output format', 'c3d1': 'Chem3D Cartesian 1 format', 'CONTCAR': 'VASP format', 'MDFF': 'MDFF format', 'gamout': 'GAMESS Output', 'mmcif': 'Macromolecular Crystallographic Info', 'txt': 'Title format', 'ct': 'ChemDraw Connection Table format', 'therm': 'Thermo format', 'log': 'Generic Output file format', 'pc': 'PubChem format', 'dmol': 'DMol3 coordinates format', 'molden': 'Molden format', 'ml2': 'Sybyl Mol2 format', 'fract': 'Free Form Fractional format', 'msi': 'Accelrys/MSI Cerius II MSI format', 'cdxml': 'ChemDraw CDXML format', 'g98': 'Gaussian Output', 'prep': 'Amber Prep format', 'gpr': 'Ghemical format', 'cub': 'Gaussian cube format', 'gam': 'GAMESS Output', 'gukin': 'GAMESS-UK Input', 'cmlr': 'CML Reaction format', 'abinit': 'ABINIT Output Format', 'POSCAR': 'VASP format', 'ins': 'ShelX format', 'tmol': 'TurboMole Coordinate format', 'png': 'PNG 2D depiction', 'cif': 'Crystallographic Information File', 'gamess': 'GAMESS Output', 'car': 'Accelrys/MSI Biosym/Insight II CAR format', 'mcif': 'Macromolecular Crystallographic Info', 'smi': 'SMILES format', 'can': 'Canonical SMILES format', 'caccrt': 'Cacao Cartesian format', 'fhiaims': 'FHIaims XYZ format', 'inp': 'GAMESS Input', 'gukout': 'GAMESS-UK Output', 'sy2': 'Sybyl Mol2 format', 'fasta': 'FASTA format', 'mpqc': 'MPQC output format', 'mold': 'Molden format', 'molf': 'Molden format', 'jout': 'Jaguar output format', 'yob': 'YASARA.org YOB format', 'mcdl': 'MCDL format', 'ent': 'Protein Data Bank format', 'adfout': 'ADF output format', 'gro': 'GRO format', 'smiles': 'SMILES format', 'fs': 'Fastsearch format', 'mol2': 'Sybyl Mol2 format', 'cdjson': 'ChemDoodle JSON', 'pqr': 'PQR format', 'g94': 'Gaussian Output', 'g92': 'Gaussian Output', 'fch': 'Gaussian formatted checkpoint file format', 'VASP': 'VASP format', 'fck': 'Gaussian formatted checkpoint file format', 'HISTORY': 'DL-POLY HISTORY', 'fsa': 'FASTA format', 'gamin': 'GAMESS Input', 'rxn': 'MDL RXN format', 'mrv': 'Chemical Markup Language', 'sdf': 'MDL MOL format', 'gal': 'Gaussian Output', 'res': 'ShelX format', 'sd': 'MDL MOL format', 'ccc': 'CCC format', 'acesout': 'ACES output format'}
{'xed': 'XED format', 'cssr': 'CSD CSSR format', 'txyz': 'Tinker XYZ format', 'text': 'Read and write raw text', 'alc': 'Alchemy format', 'report': 'Open Babel report format', 'CONTFF': 'MDFF format', 'mna': 'Multilevel Neighborhoods of Atoms (MNA)', 'feat': 'Feature format', 'acesin': 'ACES input format', 'jin': 'Jaguar input format', 'fix': 'SMILES FIX format', 'cache': 'CAChe MolStruct format', 'adf': 'ADF cartesian input format', 'pov': 'POV-Ray input format', 'cub': 'Gaussian cube format', 'pcm': 'PCModel Format', 'mopin': 'MOPAC Internal', 'mpqcin': 'MPQC simplified input format', 'mopcrt': 'MOPAC Cartesian format', 'mpd': 'MolPrint2D format', 'cube': 'Gaussian cube format', 'mpc': 'MOPAC Cartesian format', 'nul': 'Outputs nothing', 'mop': 'MOPAC Cartesian format', 'dx': 'OpenDX cube format for APBS', 'mol': 'MDL MOL format', 'inchi': 'InChI format', 'hin': 'HyperChem HIN format', 'cml': 'Chemical Markup Language', 'lpmd': 'LPMD format', 'gjf': 'Gaussian 98/03 Input', 'nw': 'NWChem input format', 'gjc': 'Gaussian 98/03 Input', 'mdl': 'MDL MOL format', 'exyz': 'Extended XYZ cartesian coordinates format', 'dalmol': 'DALTON input format', 'unixyz': 'UniChem XYZ format', 'pdbqt': 'AutoDock PDBQT format', 'gzmat': 'Gaussian Z-Matrix Input', 'pcjson': 'PubChem JSON', 'crk3d': 'Chemical Resource Kit 3D format', 'mp': 'Molpro input format', 'cacint': 'Cacao Internal format', 'tdd': 'Thermo format', 'mmod': 'MacroModel format', 'bs': 'Ball and Stick format', 'mmd': 'MacroModel format', 'box': 'Dock 3.5 Box format', 'bgf': 'MSI BGF format', 'fa': 'FASTA format', 'k': 'Compare molecules using InChI', 'POSFF': 'MDFF format', 'vmol': 'ViewMol format', 'molreport': 'Open Babel molecule report', 'crk2d': 'Chemical Resource Kit diagram(2D)', 'gr96': 'GROMOS96 format', 'CONFIG': 'DL-POLY CONFIG', 'pdb': 'Protein Data Bank format', 'ck': 'ChemKin format', 'rsmi': 'Reaction SMILES format', 'c3d2': 'Chem3D Cartesian 2 format', 'xyz': 'XYZ cartesian coordinates format', 'c3d1': 'Chem3D Cartesian 1 format', 'CONTCAR': 'VASP format', 'MDFF': 'MDFF format', 'mmcif': 'Macromolecular Crystallographic Info', 'txt': 'Title format', 'ct': 'ChemDraw Connection Table format', 'therm': 'Thermo format', 'paint': 'Painter format', 'dmol': 'DMol3 coordinates format', 'molden': 'Molden format', 'ml2': 'Sybyl Mol2 format', 'fract': 'Free Form Fractional format', 'cht': 'Chemtool format', 'zin': 'ZINDO input format', 'cdxml': 'ChemDraw CDXML format', 'gpr': 'Ghemical format', 'gau': 'Gaussian 98/03 Input', 'sdf': 'MDL MOL format', 'gukin': 'GAMESS-UK Input', 'cmlr': 'CML Reaction format', 'POSCAR': 'VASP format', 'copy': 'Copy raw text', 'tmol': 'TurboMole Coordinate format', 'png': 'PNG 2D depiction', 'confabreport': 'Confab report format', 'pointcloud': 'Point cloud on VDW surface', 'cif': 'Crystallographic Information File', 'outmol': 'DMol3 coordinates format', 'stl': 'STL 3D-printing format', 'mcif': 'Macromolecular Crystallographic Info', 'smi': 'SMILES format', 'can': 'Canonical SMILES format', 'svg': 'SVG 2D depiction', 'cac': 'CAChe MolStruct format', 'caccrt': 'Cacao Cartesian format', 'qcin': 'Q-Chem input format', 'fhiaims': 'FHIaims XYZ format', 'inp': 'GAMESS Input', 'gukout': 'GAMESS-UK Output', 'sy2': 'Sybyl Mol2 format', 'fasta': 'FASTA format', 'ascii': 'ASCII format', 'molf': 'Molden format', 'msms': "M.F. Sanner's MSMS input format", 'mold': 'Molden format', 'yob': 'YASARA.org YOB format', 'mcdl': 'MCDL format', 'fpt': 'Fingerprint format', 'ent': 'Protein Data Bank format', 'fps': 'FPS text fingerprint format (Dalke)', 'lmpdat': 'The LAMMPS data format', 'gro': 'GRO format', 'csr': 'Accelrys/MSI Quanta CSR format', 'smiles': 'SMILES format', 'inchikey': 'InChIKey', 'fs': 'Fastsearch format', 'orcainp': 'ORCA input format', 'mol2': 'Sybyl Mol2 format', 'cdjson': 'ChemDoodle JSON', 'pqr': 'PQR format', 'pqs': 'Parallel Quantum Solutions format', 'fh': 'Fenske-Hall Z-Matrix format', 'VASP': 'VASP format', 'fsa': 'FASTA format', 'gamin': 'GAMESS Input', 'rxn': 'MDL RXN format', 'com': 'Gaussian 98/03 Input', 'mrv': 'Chemical Markup Language', 'sd': 'MDL MOL format'}
Возьмем структуру порфирина в формате SMILES из ChEBI: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:8337 это структура с заданной в SMILES ароматикой, дает 4 протона у азотов после расчетов. Нам не годится.
А потом возьмем правильную из PubChem: https://pubchem.ncbi.nlm.nih.gov/compound/66868#section=Canonical-SMILES&fullscreen=true
Тут двойные связи заданы в явном виде. Это хорошо.
Прочитаем SMILES, добавим протоны, создадим черновую 3D структуру.
In [35]:
#mol=pybel.readstring('smi','c1cc2cc3ccc(cc4ccc(cc5ccc(cc1n2)[nH]5)n4)[nH]3')
mol=pybel.readstring('smi','C1=CC2=CC3=CC=C(N3)C=C4C=CC(=N4)C=C5C=CC(=N5)C=C1N2')
mol.addh()
mol.make3D(steps=10000) #чтобы получить адекватную оптимизированную структуру
mol
mol.write(format='pdb',filename='my_before.pdb',overwrite=True)
Это неправильная структура. Она не плоская и с четырьмя водородами в центре.
In [5]:
Image(filename='1.png')
Out[5]:
In [6]:
Image(filename='2.png')
Out[6]:
Это правильная структура - плоская, с двумя атомами водорода у центральных атомов азота.
In [7]:
Image(filename='3.png')
Out[7]:
Посмотрим, как оно может записывать формат программы семиэмпирических расчётов MOPAC способом PM6:
In [12]:
mop=mol.write(format='mopin',opt={'k':'PM6 CHARGE=%d' % mol.charge})
In [27]:
mop=mol.write(format='mopin',filename='my.mop',opt={'k':'PM6 CHARGE=%d' % mol.charge},overwrite=True)
Файл my.mop говорит, что заряд равен 0. Попробуем другой способ, AM1, и вывод покажем на экран:
In [22]:
mop_am1=mol.write(format='mopin',opt={'k':'AM1 CHARGE=%d' % mol.charge})
mop_am1=mol.write(format='mopin',opt={'k':'AM1 CHARGE=%d' % mol.charge},overwrite=True)
print mop_am1
AM1 CHARGE=0 C 0.000000 1 0.000000 1 0.000000 1 0 0 0 C 1.349532 1 0.000000 1 0.000000 1 1 0 0 C 1.380625 1 128.734407 1 0.000000 1 2 1 0 C 1.246192 1 118.888581 1 185.511102 1 3 2 1 C 1.323296 1 118.110177 1 9.359735 1 4 3 2 C 1.270498 1 141.539740 1 11.877331 1 5 4 3 C 1.255446 1 131.360438 1 180.208085 1 6 5 4 C 1.285514 1 95.326840 1 358.749950 1 7 6 5 C 1.366278 1 127.220982 1 180.959656 1 8 7 6 C 1.285133 1 121.412028 1 359.419856 1 9 8 7 C 1.426076 1 132.674018 1 179.747448 1 10 9 8 C 1.295418 1 113.583158 1 180.796041 1 11 10 9 C 1.351810 1 90.349497 1 11.571021 1 12 11 10 C 1.372000 1 127.522897 1 163.906933 1 13 12 11 C 1.606991 1 105.108639 1 22.922675 1 14 13 12 C 1.562527 1 126.179663 1 150.947833 1 15 14 13 C 2.073936 1 125.487845 1 99.262857 1 14 13 12 C 2.141667 1 71.847281 1 74.836588 1 17 14 13 C 2.232396 1 76.718821 1 178.724106 1 7 6 5 C 1.594036 1 84.286315 1 227.322801 1 2 1 3 N 1.217071 1 80.467866 1 329.351423 1 2 1 3 N 1.253146 1 35.510915 1 354.872329 1 17 14 13 H 0.985236 1 71.331078 1 16.816689 1 15 14 13 N 1.242861 1 120.916975 1 358.697665 1 10 9 8 N 1.296964 1 128.118877 1 191.162457 1 5 4 3 H 0.961592 1 119.514441 1 0.296534 1 25 5 4 H 1.276938 1 154.298606 1 43.402319 1 1 2 3 H 1.229417 1 100.840347 1 160.553899 1 2 1 3 H 1.027633 1 108.080539 1 192.221419 1 4 3 2 H 0.892296 1 117.372540 1 4.307063 1 6 5 4 H 1.017425 1 127.736214 1 180.420089 1 7 6 5 H 1.036646 1 124.238260 1 180.166206 1 9 8 7 H 1.016615 1 125.023620 1 0.075236 1 11 10 9 H 1.048795 1 137.902547 1 180.143396 1 12 11 10 H 1.457404 1 48.224960 1 119.502638 1 17 14 13 H 1.174719 1 163.101111 1 31.128264 1 16 15 14 H 0.498733 1 71.559740 1 290.883541 1 16 15 14 H 0.875346 1 143.476227 1 306.626554 1 20 2 1 H 1.518455 1 115.608797 1 3.463878 1 3 2 1 H 0.946387 1 138.017793 1 10.365057 1 24 10 9
Запустим MOPAC, чтобы оптимизировать структуру и получить ее в PDB файле.
In [25]:
%%bash
export MOPAC_LICENSE='/home/preps/golovin/progs/mopac/'
/home/preps/golovin/progs/mopac/MOPAC2016.exe my.mop
MOPAC Job: "my.mop" ended normally on Mar 24, 2017, at 16:24.
In [29]:
opt=pybel.readfile('mopout','my.out')
for i in opt:
print i
i.write(format='pdb',filename='my.pdb')
[C@@H]12[C@@]3([C@@H]([CH]c4ccc([CH]c5ccc(/C(=C/[C][N]#[C])/C=C)[nH]5)[nH]4)N23)C1 my.out
--------------------------------------------------------------------------- IOError Traceback (most recent call last) <ipython-input-29-4e9704e51f1b> in <module>() 2 for i in opt: 3 print i ----> 4 i.write(format='pdb',filename='my.pdb') /home/preps/golovin/miniconda2/lib/python2.7/site-packages/pybel.pyc in write(self, format, filename, overwrite, opt) 537 if not overwrite and os.path.isfile(filename): 538 raise IOError(("%s already exists. Use 'overwrite=True' to " --> 539 "overwrite it.") % filename) 540 obconversion.WriteFile(self.OBMol, filename) 541 obconversion.CloseOutFile() IOError: my.pdb already exists. Use 'overwrite=True' to overwrite it.
Теперь, убедившись, что по отдельности все работает, создадим функцию. На вход - SMILES и метод обработки, на выход - PDB файл (и еще желательно картинки, но пока непонятно, как)
In [43]:
import subprocess
def ab_initio(smiles, method, prefix):
#стоило как-то иначе назвать функцию, но не хочется все переписывать
mol=pybel.readstring('smi',smiles)
mol.addh()
mol.make3D(steps=10000)
mop=mol.write(format='mopin',opt={'k': method+' CHARGE=%d' % mol.charge})
mop=mol.write(format='mopin',filename = prefix+'.mop',opt={'k': method+' CHARGE=%d' % mol.charge},overwrite=True)
mol.write(format='pdb',filename=prefix+'_before.pdb',overwrite=True)
cmd1 = " export MOPAC_LICENSE='/home/preps/golovin/progs/mopac/' "
cmd2 = '/home/preps/golovin/progs/mopac/MOPAC2016.exe '+prefix+'.mop'
subprocess.call(cmd1, shell=True)
subprocess.call(cmd2, shell=True)
opt=pybel.readfile('mopout',prefix+'.out')
for i in opt:
print i
i.write(format='pdb',filename=prefix+'.pdb',overwrite=True)
In [44]:
ab_initio('CC(=O)C','PM6', 'acetone')
ab_initio('C1=CC2=CC3=CC=C(N3)C=C4C=CC(=N4)C=C5C=CC(=N5)C=C1N2','PM6', 'por_pm6')
ab_initio('C1=CC2=CC3=CC=C(N3)C=C4C=CC(=N4)C=C5C=CC(=N5)C=C1N2','AM1', 'por_am1')
CC(=O)C acetone.out c1c/c/2=C/c3cc/c(=C/c4ccc([n]4)/C=C\4/C=CC(=N4)/C=c/1\[nH]2)/[nH]3 por_pm6.out c1c/c/2=C/c3cc/c(=C/c4ccc([n]4)/C=C\4/C=CC(=N4)/C=c/1\[nH]2)/[nH]3 por_am1.out
Методом PM6 получился плоский порфирин, а методом AM1 - нет.
AM1:
In [10]:
Image(filename='4.png')
Out[10]:
PM6:
In [11]:
Image(filename='5.png')
Out[11]:
Это наложение структур, полученных PM6 и AM1: отличия только из-за того, что молекула AM1 не плоская.
In [12]:
Image(filename='6.png')
Out[12]:
Рассчитаем возбужденные состояния порфирина и спектр поглощения молекулы. Для этого допишем в файл my.mop (порфирин, PM6) две строчки:
In [15]:
%%bash
cp my.mop my_spectr.mop
echo "" >> my_spectr.mop
echo "cis c.i.=4 meci oldgeo" >> my_spectr.mop
echo "some description" >> my_spectr.mop
Process is terminated.
In [17]:
%%bash
export MOPAC_LICENSE='/home/preps/golovin/progs/mopac/'
/home/preps/golovin/progs/mopac/MOPAC2016.exe my_spectr.mop
MOPAC Job: "my_spectr.mop" ended normally on Apr 26, 2017, at 01:06.
In [19]:
opt=pybel.readfile('mopout','my_spectr.out')
for i in opt:
print i
i.write(format='pdb',filename='my_spectr.pdb',overwrite=True)
[C@@H]12[C@@]3([C@@H]([CH]c4ccc([CH]c5ccc(/C(=C/[C][N]#[C])/C=C)[nH]5)[nH]4)N23)C1 my_spectr.out
В конце файла приведены значения энергий для электронных переходов. На основании этих значений и простой формулы (см. ниже) рассчитаем длину волн, при которых происходят эти переходы.
In [11]:
from IPython.core.display import HTML
Image(url= "http://upload.wikimedia.org/math/2/5/2/252dadcde07fc3bb32ba42277d845707.png")
Out[11]:
In [18]:
f = open('my_spectr.out', 'r')
lines = f.readlines()[-21:-13]
f.close()
energies = [float(line.split()[1]) for line in lines]
print energies, 'eV'
[2.269214, 2.538682, 2.55168, 3.328276, 3.919001, 4.347925, 5.502005, 5.527205] eV
Получили из файла значения энергий, теперь рассчитаем соотвутствующие им длины волн и частоты
In [23]:
wavelengths = [1239.84193/e for e in energies]
frequencies = [e/4.135667516 for e in energies]
print 'frequncy,THz\t wavelength,nm\tenergy,eV'
for i in range(len(energies)):
print '%.4f \t %.4f \t %.4f' % (frequencies[i]*1000, wavelengths[i], energies[i])
frequncy,THz wavelength,nm energy,eV 548.6935 546.3751 2.2692 613.8506 488.3802 2.5387 616.9935 485.8924 2.5517 804.7736 372.5178 3.3283 947.6103 316.3668 3.9190 1051.3236 285.1572 4.3479 1330.3789 225.3437 5.5020 1336.4723 224.3163 5.5272
Часть 1.2. Тимидиновые димеры¶
Дан .pdb файл тиминового димера. Известно, что ультрафиолет может превращать тимины в тиминовые димеры, также известно, что ДНК фотолиаза при облучении ультрафиолетом востановливает основания тиминов до нормального. Наша цель - увидеть переход из димера в тимины при возбуждении системы. Так как вычисление возбуждённых состояний в MOPAC затруднены, мы имитируем возбуждение ионизируя оба кольца, т.е. указывая заряд системы +2. И полученое возбуждённое состояние снова оптимизируем при заряде 0.
Это исходная структура димера:
In [18]:
Image(filename='7.png')
Out[18]:
In [24]:
import pybel
mol=pybel.readfile("pdb", "td.pdb").next()
mop=mol.write(format='mop',filename='td.mop',opt={'k':'PM6 CHARGE=%d' % mol.charge},overwrite=True)
Пробую в разных координатах: внутренних и картезианских. Результат один - ничего не выдается. А все потому, что в оптимизированной структуре неправильно прописан столбец имен атомов. Скопировала из исходного файла - все заработало.
In [25]:
%%bash
export MOPAC_LICENSE='/home/preps/golovin/progs/mopac/'
/home/preps/golovin/progs/mopac/MOPAC2016.exe td.mop
MOPAC Job: "td.mop" ended normally on Apr 26, 2017, at 21:27.
In [26]:
opt=pybel.readfile('mopout','td.out')
for i in opt:
print i
i.write(format='pdb',filename='td_opt.pdb',overwrite=True)
N1[C@H]2[C@@](C)(C(=O)NC1=O)[C@@]1([C@H]2NC(=O)NC1=O)C td.out
Это исходная (желтая) и оптимизированная (белая) структура. Отличия в геометрии небольшие.
In [28]:
Image(filename='8.png')
Out[28]:
Оптимизируем результат при заряде +2 (имитируем возбуждённое состояние):
In [29]:
%%bash
cp td.mop td2.mop
#change line PM6 CHARGE=0 to PM6 CHARGE=+2
In [30]:
! /home/preps/golovin/progs/mopac/MOPAC2016.exe td2.mop
MOPAC Job: "td2.mop" ended normally on Apr 26, 2017, at 21:28.
In [31]:
opt=pybel.readfile('mopout','td2.out')
for i in opt:
print i
i.write(format='pdb',filename='td2_opt.pdb',overwrite=True)
N1[CH][C@@](C)(C(=O)NC1=O)[C@@]1([CH]NC(=O)NC1=O)C td2.out
Открываем и видим два тимина, соединенных теперь уже одной связью:
In [32]:
Image(filename='9.png')
Out[32]:
Теперь возьмем структуру этих полусоединенных тиминов и оптимизируем ее с зарядом системы 0.
In [33]:
mol=pybel.readfile("pdb", "td2_opt.pdb").next()
mop=mol.write(format='mop',filename='td2_opt.mop',opt={'k':'PM6 CHARGE=%d' % mol.charge},overwrite=True)
In [34]:
! /home/preps/golovin/progs/mopac/MOPAC2016.exe td2_opt.mop
MOPAC Job: "td2_opt.mop" ended normally on Apr 26, 2017, at 21:29.
In [35]:
opt=pybel.readfile('mopout','td2_opt.out')
for i in opt:
print i
i.write(format='pdb',filename='td2_last.pdb',overwrite=True)
[nH]1cc(C)c(=O)[nH]c1=O.[nH]1cc(C)c(=O)[nH]c1=O td2_opt.out
Получились свободные тимины:
In [36]:
Image(filename='10.png')
Out[36]:
Энергии всех состояний:
In [40]:
%%bash
echo dimer
grep 'TOTAL ENERGY' td.out
echo semi-dimer
grep 'TOTAL ENERGY' td2.out
echo two thymins
grep 'TOTAL ENERGY' td2_opt.out
dimer
TOTAL ENERGY = -3273.57488 EV
semi-dimer
TOTAL ENERGY = -3253.90524 EV
two thymins
TOTAL ENERGY = -3273.70216 EV
Как следует из рисунков, при возбуждении системы тиминовый димер разрушился только наполовину. Однако, возбуждённое состояние оказалось переходным, из которого система может свалиться как в тиминовые нуклеотиды, так и обратно в димер. А так как система из двух тиминов (-3273.7 eV) оказалась чуть более выгодным, чем система из димера (-3273.6 eV), то она свалилась именно в тимины.
Часть 2. Ab initio вычисления: Gamess US¶
Найдём оптимальную геометрию для нафталена и азулена и рассчитаем теплоты образования этих молекул разными подходами квантовой механики. Для этого нужно:
1) Построить и оптимизировать с помощью MOPAC структуры нафталена и азулена
2) Создать входные файлы для Gamess.
Нафтален: https://pubchem.ncbi.nlm.nih.gov/compound/931#section=Canonical-SMILES&fullscreen=true
Азулен: https://pubchem.ncbi.nlm.nih.gov/compound/9231#section=Canonical-SMILES&fullscreen=true
Заметим, что они отличаются перестановкой двух символов.
In [45]:
ab_initio('C1=CC=C2C=CC=CC2=C1','PM6','na')
ab_initio('C1=CC=C2C=CC=C2C=C1','PM6','az')
c1ccc2ccccc2c1 na.out c1ccc2ccccc2c1 az.out
Покажем результаты до и после оптимизации в PyMOL с параметром set valence, on
Молекула азулена превращается в молекулу нафталена.
Азулен до и после оптимизации MOPAC:
In [47]:
Image(filename='11.png')
Out[47]:
In [48]:
Image(filename='12.png')
Out[48]:
Нафтален до и после оптимизации MOPAC:
In [49]:
Image(filename='13.png')
Out[49]:
In [50]:
Image(filename='14.png')
Out[50]:
А если поискать структуры с заданной ароматикой?
Нафтален: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:16482 Азулен: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:31249
In [54]:
ab_initio('c1ccc2ccccc2c1','PM6','na_ar')
ab_initio('c1ccc2cccc2cc1','PM6','az_ar')
c1ccc2ccccc2c1 na_ar.out c1ccc2ccccc2c1 az_ar.out
В геометрии азулена до и после оптимизации ничего не изменилось. Все тот же нафтален и до, и после оптимизации. Будем работать только с нафталеном. Создадим входные файлы для Gamess. В файле orca.inp добавим заголовок !HF RHF OPT 6-31G - это означает, что работаем ограниченным методом Хартри-Фока в базисе 6-31G. На этих данных запустим ORCA, чтобы оптимизировать геометрию молекулы нафталена.
In [5]:
opt=pybel.readfile('mopout','na_ar.out')
for i in opt:
print i
i.write(format='orcainp',filename='orca.inp',overwrite=True)
c1ccc2ccccc2c1 na_ar.out
In [9]:
%%bash
/srv/databases/orca/orca orca.inp | tee orca-opt.log
*****************
* O R C A *
*****************
--- An Ab Initio, DFT and Semiempirical electronic structure package ---
#######################################################
# -***- #
# Department of molecular theory and spectroscopy #
# Directorship: Frank Neese #
# Max Planck Institute for Chemical Energy Conversion #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
Program Version 3.0.3 - RELEASE -
With contributions from (in alphabetic order):
Ute Becker : Parallelization
Dmytro Bykov : SCF Hessian
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Dimitrios Liakos : Extrapolation schemes; parallel MDCI
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density
Simone Kossmann : Meta GGA functionals, TD-DFT gradient, OOMP2, MP2 Hessian
Taras Petrenko : DFT Hessian,TD-DFT gradient, ASA and ECA modules, normal mode analysis, Resonance Raman, ABS, FL, XAS/XES, NRVS
Christoph Reimann : Effective Core Potentials
Michael Roemelt : Restricted open shell CIS
Christoph Riplinger : Improved optimizer, TS searches, QM/MM, DLPNO-CCSD
Barbara Sandhoefer : DKH picture change effects
Igor Schapiro : Molecular dynamics
Kantharuban Sivalingam : CASSCF convergence, NEVPT2
Boris Wezisla : Elementary symmetry handling
Frank Wennmohs : Technical directorship
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Stefan Grimme, W. Hujo, H. Kruse, T. Risthaus : VdW corrections, initial TS optimization,
DFT functionals, gCP
Ed Valeev : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Andreas Klamt, Michael Diedenhofen : otool_cosmo (COSMO solvation model)
Frank Weinhold : gennbo (NPA and NBO analysis)
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
SCALAPACK package : Parallel linear algebra routines
Your calculation utilizes the basis: 6-31G
Cite in your paper:
H - He: W.J. Hehre, R. Ditchfield and J.A. Pople, J. Chem. Phys. 56,
Li - Ne: 2257 (1972). Note: Li and B come from J.D. Dill and J.A.
Pople, J. Chem. Phys. 62, 2921 (1975).
Na - Ar: M.M. Francl, W.J. Pietro, W.J. Hehre, J.S. Binkley, M.S. Gordon,
D.J. DeFrees and J.A. Pople, J. Chem. Phys. 77, 3654 (1982)
K - Zn: V. Rassolov, J.A. Pople, M. Ratner and T.L. Windus, J. Chem. Phys.
(accepted, 1998)
Note: He and Ne are unpublished basis sets taken from the Gaussian program
================================================================================
WARNINGS
Please study these warnings very carefully!
================================================================================
Now building the actual basis set
WARNING: Geometry Optimization
===> : Switching off AutoStart
For restart on a previous wavefunction, please use MOREAD
INFO : the flag for use of LIBINT has been found!
================================================================================
INPUT FILE
================================================================================
NAME = orca.inp
| 1> # ORCA input file
| 2> # na_ar.out
| 3> !HF RHF OPT 6-31G
| 4> * xyz 0 1
| 5> C -0.05678 -0.03497 -0.03698
| 6> C 1.36912 -0.03497 -0.03698
| 7> C 2.06233 1.14935 -0.03698
| 8> C 1.36421 2.39853 -0.03729
| 9> C 2.06068 3.64916 -0.03782
| 10> C 1.36601 4.83230 -0.03539
| 11> C -0.06018 4.83073 -0.03283
| 12> C -0.75337 3.64707 -0.03455
| 13> C -0.05524 2.39765 -0.03623
| 14> C -0.75233 1.14744 -0.03646
| 15> H -0.57884 -0.99046 -0.03733
| 16> H 1.89233 -0.98964 -0.03668
| 17> H 3.15102 1.15957 -0.03669
| 18> H 3.14956 3.63994 -0.04052
| 19> H 1.88786 5.78761 -0.03506
| 20> H -0.58375 5.78525 -0.03022
| 21> H -1.84216 3.63593 -0.03418
| 22> H -1.84093 1.15662 -0.03608
| 23> *
| 24>
| 25> ****END OF INPUT****
================================================================================
*****************************
* Geometry Optimization Run *
*****************************
Geometry optimization settings:
Update method Update .... BFGS
Choice of coordinates CoordSys .... Redundant Internals
Initial Hessian InHess .... Almoef's Model
Convergence Tolerances:
Energy Change TolE .... 5.0000e-06 Eh
Max. Gradient TolMAXG .... 3.0000e-04 Eh/bohr
RMS Gradient TolRMSG .... 1.0000e-04 Eh/bohr
Max. Displacement TolMAXD .... 4.0000e-03 bohr
RMS Displacement TolRMSD .... 2.0000e-03 bohr
------------------------------------------------------------------------------
ORCA OPTIMIZATION COORDINATE SETUP
------------------------------------------------------------------------------
The optimization will be done in new redundant internal coordinates
Making redundant internal coordinates ... (new redundants) done
Evaluating the initial hessian ... (Almloef) done
Evaluating the coordinates ... done
Calculating the B-matrix .... done
Calculating the G-matrix .... done
Diagonalizing the G-matrix .... done
The first mode is .... 45
The number of degrees of freedom .... 48
-----------------------------------------------------------------
Redundant Internal Coordinates
-----------------------------------------------------------------
Definition Initial Value Approx d2E/dq
-----------------------------------------------------------------
1. B(C 1,C 0) 1.4259 0.547599
2. B(C 2,C 1) 1.3723 0.666820
3. B(C 3,C 2) 1.4310 0.537392
4. B(C 4,C 3) 1.4315 0.536480
5. B(C 5,C 4) 1.3720 0.667500
6. B(C 6,C 5) 1.4262 0.547009
7. B(C 7,C 6) 1.3717 0.668239
8. B(C 8,C 7) 1.4312 0.536967
9. B(C 8,C 3) 1.4195 0.560728
10. B(C 9,C 8) 1.4314 0.536609
11. B(C 9,C 0) 1.3718 0.667955
12. B(H 10,C 0) 1.0888 0.361677
13. B(H 11,C 1) 1.0886 0.361900
14. B(H 12,C 2) 1.0887 0.361773
15. B(H 13,C 4) 1.0889 0.361528
16. B(H 14,C 5) 1.0886 0.362021
17. B(H 15,C 6) 1.0887 0.361840
18. B(H 16,C 7) 1.0888 0.361628
19. B(H 17,C 9) 1.0886 0.361905
20. A(C 9,C 0,H 10) 120.8826 0.357662
21. A(C 1,C 0,H 10) 118.6513 0.345849
22. A(C 1,C 0,C 9) 120.4661 0.430208
23. A(C 0,C 1,C 2) 120.3414 0.430077
24. A(C 2,C 1,H 11) 120.9335 0.357596
25. A(C 0,C 1,H 11) 118.7251 0.345884
26. A(C 1,C 2,C 3) 120.4594 0.428627
27. A(C 1,C 2,H 12) 120.8793 0.357575
28. A(C 3,C 2,H 12) 118.6614 0.344773
29. A(C 2,C 3,C 4) 121.6876 0.412314
30. A(C 2,C 3,C 8) 119.1637 0.415565
31. A(C 4,C 3,C 8) 119.1488 0.415439
32. A(C 5,C 4,H 13) 120.9042 0.357596
33. A(C 3,C 4,H 13) 118.6281 0.344635
34. A(C 3,C 4,C 5) 120.4677 0.428575
35. A(C 6,C 5,H 14) 118.7091 0.345841
36. A(C 4,C 5,H 14) 120.9349 0.357679
37. A(C 4,C 5,C 6) 120.3560 0.430072
38. A(C 7,C 6,H 15) 120.8999 0.357716
39. A(C 5,C 6,H 15) 118.6826 0.345812
40. A(C 5,C 6,C 7) 120.4175 0.430158
41. A(C 8,C 7,H 16) 118.6087 0.344704
42. A(C 6,C 7,H 16) 120.9408 0.357680
43. A(C 6,C 7,C 8) 120.4506 0.428730
44. A(C 7,C 8,C 9) 121.6620 0.412273
45. A(C 3,C 8,C 9) 119.1786 0.415457
46. A(C 3,C 8,C 7) 119.1594 0.415506
47. A(C 8,C 9,H 17) 118.6599 0.344709
48. A(C 0,C 9,H 17) 120.9492 0.357701
49. A(C 0,C 9,C 8) 120.3908 0.428646
50. D(H 11,C 1,C 0,H 10) -0.0390 0.020507
51. D(C 2,C 1,C 0,C 9) -0.0252 0.020507
52. D(H 11,C 1,C 0,C 9) 179.9568 0.020507
53. D(C 2,C 1,C 0,H 10) 179.9790 0.020507
54. D(C 3,C 2,C 1,C 0) -0.0144 0.031075
55. D(H 12,C 2,C 1,H 11) 0.0006 0.031075
56. D(C 3,C 2,C 1,H 11) -179.9960 0.031075
57. D(H 12,C 2,C 1,C 0) 179.9822 0.031075
58. D(C 8,C 3,C 2,H 12) -179.9335 0.019727
59. D(C 4,C 3,C 2,H 12) 0.0279 0.019727
60. D(C 4,C 3,C 2,C 1) -179.9754 0.019727
61. D(C 8,C 3,C 2,C 1) 0.0632 0.019727
62. D(H 13,C 4,C 3,C 2) 0.1518 0.019658
63. D(C 5,C 4,C 3,C 8) 0.0931 0.019658
64. D(C 5,C 4,C 3,C 2) -179.8683 0.019658
65. D(H 13,C 4,C 3,C 8) -179.8869 0.019658
66. D(H 14,C 5,C 4,H 13) -0.0643 0.031143
67. D(H 14,C 5,C 4,C 3) 179.9563 0.031143
68. D(C 6,C 5,C 4,H 13) 179.9549 0.031143
69. D(C 6,C 5,C 4,C 3) -0.0246 0.031143
70. D(H 15,C 6,C 5,H 14) -0.0242 0.020462
71. D(H 15,C 6,C 5,C 4) 179.9571 0.020462
72. D(C 7,C 6,C 5,H 14) 179.9324 0.020462
73. D(C 7,C 6,C 5,C 4) -0.0863 0.020462
74. D(H 16,C 7,C 6,H 15) 0.0513 0.031217
75. D(H 16,C 7,C 6,C 5) -179.9043 0.031217
76. D(C 8,C 7,C 6,H 15) -179.9187 0.031217
77. D(C 8,C 7,C 6,C 5) 0.1257 0.031217
78. D(C 9,C 8,C 3,C 2) -0.0725 0.021539
79. D(C 7,C 8,C 3,C 4) -0.0536 0.021539
80. D(C 7,C 8,C 3,C 2) 179.9088 0.021539
81. D(C 9,C 8,C 7,H 16) -0.0452 0.019695
82. D(C 9,C 8,C 7,C 6) 179.9255 0.019695
83. D(C 3,C 8,C 7,H 16) 179.9740 0.019695
84. D(C 3,C 8,C 7,C 6) -0.0553 0.019695
85. D(C 9,C 8,C 3,C 4) 179.9651 0.021539
86. D(H 17,C 9,C 8,C 7) 0.0455 0.019668
87. D(C 0,C 9,C 8,C 7) -179.9464 0.019668
88. D(C 0,C 9,C 8,C 3) 0.0344 0.019668
89. D(H 17,C 9,C 0,H 10) 0.0188 0.031189
90. D(H 17,C 9,C 0,C 1) -179.9769 0.031189
91. D(H 17,C 9,C 8,C 3) -179.9737 0.019668
92. D(C 8,C 9,C 0,H 10) -179.9895 0.031189
93. D(C 8,C 9,C 0,C 1) 0.0148 0.031189
-----------------------------------------------------------------
Number of atoms .... 18
Number of degrees of freedom .... 93
*************************************************************
* GEOMETRY OPTIMIZATION CYCLE 1 *
*************************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C -0.056780 -0.034970 -0.036980
C 1.369120 -0.034970 -0.036980
C 2.062330 1.149350 -0.036980
C 1.364210 2.398530 -0.037290
C 2.060680 3.649160 -0.037820
C 1.366010 4.832300 -0.035390
C -0.060180 4.830730 -0.032830
C -0.753370 3.647070 -0.034550
C -0.055240 2.397650 -0.036230
C -0.752330 1.147440 -0.036460
H -0.578840 -0.990460 -0.037330
H 1.892330 -0.989640 -0.036680
H 3.151020 1.159570 -0.036690
H 3.149560 3.639940 -0.040520
H 1.887860 5.787610 -0.035060
H -0.583750 5.785250 -0.030220
H -1.842160 3.635930 -0.034180
H -1.840930 1.156620 -0.036080
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 -0.107298649884049 -0.066083722903226 -0.069882072432408
1 C 6.0000 0 12.011 2.587261844474264 -0.066083722903226 -0.069882072432408
2 C 6.0000 0 12.011 3.897238897769815 2.171956732022391 -0.069882072432408
3 C 6.0000 0 12.011 2.577983289156711 4.532564823994139 -0.070467887533923
4 C 6.0000 0 12.011 3.894120849648845 6.895913018860075 -0.071469442384902
5 C 6.0000 0 12.011 2.581384796197769 9.131723596947664 -0.066877407879473
6 C 6.0000 0 12.011 -0.113723718739381 9.128756726917407 -0.062039708976635
7 C 6.0000 0 12.011 -1.423662977512253 6.891963491240179 -0.065290037926979
8 C 6.0000 0 12.011 -0.104388471637810 4.530901864996289 -0.068464777831967
9 C 6.0000 0 12.011 -1.421697662332975 2.168347355106601 -0.068899414842769
10 H 1.0000 0 1.008 -1.093849075358977 -1.871698146603643 -0.070543476579280
11 H 1.0000 0 1.008 3.575985455003202 -1.870148571173827 -0.069315154592232
12 H 1.0000 0 1.008 5.954564842508542 2.191269733111066 -0.069334051853571
13 H 1.0000 0 1.008 5.951805842353018 6.878489743905321 -0.076571702946489
14 H 1.0000 0 1.008 3.567538379184574 10.936997869943974 -0.066253798255279
15 H 1.0000 0 1.008 -1.103127630676531 10.932538116267921 -0.057107523767100
16 H 1.0000 0 1.008 -3.481177894864373 6.870911942108297 -0.064590839257428
17 H 1.0000 0 1.008 -3.478853531719650 2.185695041015998 -0.068181318911879
--------------------------------
INTERNAL COORDINATES (ANGSTROEM)
--------------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 1.425900 0.000 0.000
C 2 1 0 1.372281 120.341 0.000
C 3 2 1 1.431021 120.459 0.000
C 4 3 2 1.431484 121.688 180.025
C 5 4 3 1.372003 120.468 180.132
C 6 5 4 1.426193 120.356 359.975
C 7 6 5 1.371702 120.417 359.914
C 4 3 2 1.419451 119.164 0.063
C 1 2 3 1.371818 120.466 359.975
H 1 2 3 1.088810 118.651 179.979
H 2 1 3 1.088643 118.725 179.982
H 3 2 1 1.088738 120.879 179.982
H 5 4 3 1.088922 118.628 0.152
H 6 5 4 1.088552 120.935 179.956
H 7 6 5 1.088688 118.683 179.957
H 8 7 6 1.088847 120.941 180.096
H 10 1 2 1.088639 120.949 180.023
---------------------------
INTERNAL COORDINATES (A.U.)
---------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 2.694560 0.000 0.000
C 2 1 0 2.593234 120.341 0.000
C 3 2 1 2.704239 120.459 0.000
C 4 3 2 2.705113 121.688 180.025
C 5 4 3 2.592710 120.468 180.132
C 6 5 4 2.695114 120.356 359.975
C 7 6 5 2.592141 120.417 359.914
C 4 3 2 2.682373 119.164 0.063
C 1 2 3 2.592360 120.466 359.975
H 1 2 3 2.057553 118.651 179.979
H 2 1 3 2.057237 118.725 179.982
H 3 2 1 2.057417 120.879 179.982
H 5 4 3 2.057765 118.628 0.152
H 6 5 4 2.057065 120.935 179.956
H 7 6 5 2.057321 118.683 179.957
H 8 7 6 2.057623 120.941 180.096
H 10 1 2 2.057229 120.949 180.023
---------------------
BASIS SET INFORMATION
---------------------
There are 2 groups of distinct atoms
Group 1 Type C : 10s4p contracted to 3s2p pattern {631/31}
Group 2 Type H : 4s contracted to 2s pattern {31}
Atom 0C basis set group => 1
Atom 1C basis set group => 1
Atom 2C basis set group => 1
Atom 3C basis set group => 1
Atom 4C basis set group => 1
Atom 5C basis set group => 1
Atom 6C basis set group => 1
Atom 7C basis set group => 1
Atom 8C basis set group => 1
Atom 9C basis set group => 1
Atom 10H basis set group => 2
Atom 11H basis set group => 2
Atom 12H basis set group => 2
Atom 13H basis set group => 2
Atom 14H basis set group => 2
Atom 15H basis set group => 2
Atom 16H basis set group => 2
Atom 17H basis set group => 2
------------------------------------------------------------------------------
ORCA GTO INTEGRAL CALCULATION
------------------------------------------------------------------------------
BASIS SET STATISTICS AND STARTUP INFO
# of primitive gaussian shells ... 172
# of primitive gaussian functions ... 252
# of contracted shell ... 66
# of contracted basis functions ... 106
Highest angular momentum ... 1
Maximum contraction depth ... 6
Integral package used ... LIBINT
Integral threshhold Thresh ... 2.500e-11
Primitive cut-off TCut ... 2.500e-12
INTEGRAL EVALUATION
One electron integrals ... done
Pre-screening matrix ... done
Shell pair data ... done ( 0.003 sec)
-------------------------------------------------------------------------------
ORCA SCF
-------------------------------------------------------------------------------
------------
SCF SETTINGS
------------
Hamiltonian:
Ab initio Hamiltonian Method .... Hartree-Fock(GTOs)
General Settings:
Integral files IntName .... orca
Hartree-Fock type HFTyp .... RHF
Total Charge Charge .... 0
Multiplicity Mult .... 1
Number of Electrons NEL .... 68
Basis Dimension Dim .... 106
Nuclear Repulsion ENuc .... 456.5587927602 Eh
Convergence Acceleration:
DIIS CNVDIIS .... on
Start iteration DIISMaxIt .... 12
Startup error DIISStart .... 0.200000
# of expansion vecs DIISMaxEq .... 5
Bias factor DIISBfac .... 1.050
Max. coefficient DIISMaxC .... 10.000
Newton-Raphson CNVNR .... off
SOSCF CNVSOSCF .... on
Start iteration SOSCFMaxIt .... 150
Startup grad/error SOSCFStart .... 0.003300
Level Shifting CNVShift .... on
Level shift para. LevelShift .... 0.2500
Turn off err/grad. ShiftErr .... 0.0010
Zerner damping CNVZerner .... off
Static damping CNVDamp .... on
Fraction old density DampFac .... 0.7000
Max. Damping (<1) DampMax .... 0.9800
Min. Damping (>=0) DampMin .... 0.0000
Turn off err/grad. DampErr .... 0.1000
Fernandez-Rico CNVRico .... off
SCF Procedure:
Maximum # iterations MaxIter .... 125
SCF integral mode SCFMode .... Direct
Integral package .... LIBINT
Reset frequeny DirectResetFreq .... 20
Integral Threshold Thresh .... 2.500e-11 Eh
Primitive CutOff TCut .... 2.500e-12 Eh
Convergence Tolerance:
Convergence Check Mode ConvCheckMode .... Total+1el-Energy
Energy Change TolE .... 1.000e-08 Eh
1-El. energy change .... 1.000e-05 Eh
Orbital Gradient TolG .... 1.000e-05
Orbital Rotation angle TolX .... 1.000e-05
DIIS Error TolErr .... 5.000e-07
Diagonalization of the overlap matrix:
Smallest eigenvalue ... 4.155e-04
Time for diagonalization ... 0.027 sec
Threshold for overlap eigenvalues ... 1.000e-08
Number of eigenvalues below threshold ... 0
Time for construction of square roots ... 0.001 sec
Total time needed ... 0.028 sec
-------------------
DFT GRID GENERATION
-------------------
General Integration Accuracy IntAcc ... 4.340
Radial Grid Type RadialGrid ... Gauss-Chebyshev
Angular Grid (max. acc.) AngularGrid ... Lebedev-110
Angular grid pruning method GridPruning ... 3 (G Style)
Weight generation scheme WeightScheme... Becke
Basis function cutoff BFCut ... 1.0000e-11
Integration weight cutoff WCut ... 1.0000e-14
Grids for H and He will be reduced by one unit
# of grid points (after initial pruning) ... 22912 ( 0.0 sec)
# of grid points (after weights+screening) ... 20986 ( 0.2 sec)
nearest neighbour list constructed ... 0.0 sec
Grid point re-assignment to atoms done ... 0.0 sec
Grid point division into batches done ... 0.0 sec
Reduced shell lists constructed in 0.5 sec
Total number of grid points ... 20986
Total number of batches ... 341
Average number of points per batch ... 61
Average number of grid points per atom ... 1166
Average number of shells per batch ... 46.69 (70.75%)
Average number of basis functions per batch ... 80.31 (75.77%)
Average number of large shells per batch ... 35.94 (76.98%)
Average number of large basis fcns per batch ... 63.48 (79.04%)
Maximum spatial batch extension ... 17.72, 20.37, 25.60 au
Average spatial batch extension ... 3.36, 3.42, 5.26 au
Time for grid setup = 0.673 sec
------------------------------
INITIAL GUESS: MODEL POTENTIAL
------------------------------
Loading Hartree-Fock densities ... done
Calculating cut-offs ... done
Setting up the integral package ... done
Initializing the effective Hamiltonian ... done
Starting the Coulomb interaction ... done ( 0.4 sec)
Reading the grid ... done
Mapping shells ... done
Starting the XC term evaluation ... done ( 0.4 sec)
Transforming the Hamiltonian ... done ( 0.0 sec)
Diagonalizing the Hamiltonian ... done ( 0.0 sec)
Back transforming the eigenvectors ... done ( 0.0 sec)
Now organizing SCF variables ... done
------------------
INITIAL GUESS DONE ( 1.7 sec)
------------------
--------------
SCF ITERATIONS
--------------
ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp
*** Starting incremental Fock matrix formation ***
0 -382.9203543057 0.000000000000 0.04003836 0.00388864 0.1455957 0.7000
1 -383.0210441826 -0.100689876914 0.03232926 0.00308139 0.0981123 0.7000
***Turning on DIIS***
2 -383.0856377804 -0.064593597766 0.08340258 0.00731537 0.0606378 0.0000
3 -382.7410971506 0.344540629839 0.01375200 0.00139022 0.0192604 0.0000
*** Initiating the SOSCF procedure ***
*** Shutting down DIIS ***
*** Re-Reading the Fockian ***
*** Removing any level shift ***
ITER Energy Delta-E Grad Rot Max-DP RMS-DP
4 -383.17767764 -0.4365804937 0.002971 0.002971 0.004609 0.000466
*** Restarting incremental Fock matrix formation ***
5 -383.22008075 -0.0424031031 0.001923 0.003816 0.002090 0.000184
6 -383.22013726 -0.0000565092 0.000949 0.003538 0.002154 0.000127
7 -383.22015335 -0.0000160928 0.000196 0.000450 0.000354 0.000028
8 -383.22015415 -0.0000008017 0.000069 0.000095 0.000101 0.000011
9 -383.22015428 -0.0000001295 0.000017 0.000036 0.000026 0.000003
10 -383.22015429 -0.0000000099 0.000006 0.000007 0.000006 0.000001
***Gradient check signals convergence***
***Rediagonalizing the Fockian in SOSCF/NRSCF***
*****************************************************
* SUCCESS *
* SCF CONVERGED AFTER 11 CYCLES *
*****************************************************
----------------
TOTAL SCF ENERGY
----------------
Total Energy : -383.22015429 Eh -10427.95055 eV
Components:
Nuclear Repulsion : 456.55879276 Eh 12423.59635 eV
Electronic Energy : -839.77894705 Eh -22851.54690 eV
One Electron Energy: -1422.13892753 Eh -38698.36761 eV
Two Electron Energy: 582.35998048 Eh 15846.82071 eV
Virial components:
Potential Energy : -766.43158247 Eh -20855.66364 eV
Kinetic Energy : 383.21142818 Eh 10427.71310 eV
Virial Ratio : 2.00002277
---------------
SCF CONVERGENCE
---------------
Last Energy change ... -9.8316e-10 Tolerance : 1.0000e-08
Last MAX-Density change ... 1.2897e-06 Tolerance : 1.0000e-07
Last RMS-Density change ... 9.7304e-08 Tolerance : 5.0000e-09
Last Orbital Gradient ... 8.0759e-07 Tolerance : 1.0000e-05
Last Orbital Rotation ... 7.0233e-07 Tolerance : 1.0000e-05
**** THE GBW FILE WAS UPDATED (orca.gbw) ****
**** DENSITY FILE WAS UPDATED (orca.scfp.tmp) ****
**** ENERGY FILE WAS UPDATED (orca.en.tmp) ****
----------------
ORBITAL ENERGIES
----------------
NO OCC E(Eh) E(eV)
0 2.0000 -11.250569 -306.1436
1 2.0000 -11.249542 -306.1156
2 2.0000 -11.242548 -305.9253
3 2.0000 -11.242504 -305.9241
4 2.0000 -11.242365 -305.9203
5 2.0000 -11.242294 -305.9184
6 2.0000 -11.241118 -305.8864
7 2.0000 -11.241096 -305.8858
8 2.0000 -11.240334 -305.8650
9 2.0000 -11.240323 -305.8647
10 2.0000 -1.176140 -32.0044
11 2.0000 -1.109640 -30.1948
12 2.0000 -1.048144 -28.5215
13 2.0000 -1.006949 -27.4005
14 2.0000 -0.982326 -26.7305
15 2.0000 -0.850100 -23.1324
16 2.0000 -0.833177 -22.6719
17 2.0000 -0.811822 -22.0908
18 2.0000 -0.701155 -19.0794
19 2.0000 -0.697564 -18.9817
20 2.0000 -0.676653 -18.4127
21 2.0000 -0.619752 -16.8643
22 2.0000 -0.608967 -16.5708
23 2.0000 -0.582026 -15.8377
24 2.0000 -0.581880 -15.8338
25 2.0000 -0.561812 -15.2877
26 2.0000 -0.530363 -14.4319
27 2.0000 -0.516635 -14.0583
28 2.0000 -0.480634 -13.0787
29 2.0000 -0.470657 -12.8072
30 2.0000 -0.444516 -12.0959
31 2.0000 -0.381394 -10.3783
32 2.0000 -0.317174 -8.6307
33 2.0000 -0.287347 -7.8191
34 0.0000 0.097698 2.6585
35 0.0000 0.130076 3.5395
36 0.0000 0.186591 5.0774
37 0.0000 0.235183 6.3996
38 0.0000 0.256759 6.9868
39 0.0000 0.261471 7.1150
40 0.0000 0.283593 7.7170
41 0.0000 0.307666 8.3720
42 0.0000 0.314403 8.5554
43 0.0000 0.321432 8.7466
44 0.0000 0.332737 9.0542
45 0.0000 0.354749 9.6532
46 0.0000 0.409140 11.1333
47 0.0000 0.410254 11.1636
48 0.0000 0.463321 12.6076
49 0.0000 0.483007 13.1433
50 0.0000 0.494903 13.4670
51 0.0000 0.498261 13.5584
52 0.0000 0.514050 13.9880
53 0.0000 0.537861 14.6359
54 0.0000 0.698862 19.0170
55 0.0000 0.717908 19.5353
56 0.0000 0.740382 20.1468
57 0.0000 0.744894 20.2696
58 0.0000 0.749221 20.3873
59 0.0000 0.771269 20.9873
60 0.0000 0.779272 21.2051
61 0.0000 0.789674 21.4881
62 0.0000 0.806732 21.9523
63 0.0000 0.811868 22.0921
64 0.0000 0.828405 22.5421
65 0.0000 0.858552 23.3624
66 0.0000 0.859907 23.3993
67 0.0000 0.869888 23.6709
68 0.0000 0.876571 23.8527
69 0.0000 0.880039 23.9471
70 0.0000 0.898203 24.4413
71 0.0000 0.904985 24.6259
72 0.0000 0.910699 24.7814
73 0.0000 0.920368 25.0445
74 0.0000 0.940582 25.5945
75 0.0000 0.941409 25.6170
76 0.0000 1.006064 27.3764
77 0.0000 1.078147 29.3379
78 0.0000 1.112027 30.2598
79 0.0000 1.121168 30.5085
80 0.0000 1.128962 30.7206
81 0.0000 1.129915 30.7465
82 0.0000 1.151085 31.3226
83 0.0000 1.175704 31.9925
84 0.0000 1.179653 32.1000
85 0.0000 1.215386 33.0723
86 0.0000 1.219943 33.1963
87 0.0000 1.236557 33.6484
88 0.0000 1.266588 34.4656
89 0.0000 1.302839 35.4521
90 0.0000 1.307677 35.5837
91 0.0000 1.347830 36.6763
92 0.0000 1.348665 36.6990
93 0.0000 1.358257 36.9600
94 0.0000 1.385231 37.6940
95 0.0000 1.428565 38.8732
96 0.0000 1.494145 40.6577
97 0.0000 1.502478 40.8845
98 0.0000 1.561977 42.5036
99 0.0000 1.622885 44.1609
100 0.0000 1.724057 46.9140
101 0.0000 1.755980 47.7827
102 0.0000 1.784245 48.5518
103 0.0000 1.827428 49.7268
104 0.0000 2.186521 59.4983
105 0.0000 2.187889 59.5355
********************************
* MULLIKEN POPULATION ANALYSIS *
********************************
-----------------------
MULLIKEN ATOMIC CHARGES
-----------------------
0 C : -0.210079
1 C : -0.209436
2 C : -0.165681
3 C : -0.073071
4 C : -0.165262
5 C : -0.209637
6 C : -0.209816
7 C : -0.165364
8 C : -0.073720
9 C : -0.164845
10 H : 0.201290
11 H : 0.201706
12 H : 0.210132
13 H : 0.210139
14 H : 0.201631
15 H : 0.201437
16 H : 0.210198
17 H : 0.210377
Sum of atomic charges: 0.0000000
--------------------------------
MULLIKEN REDUCED ORBITAL CHARGES
--------------------------------
0 C s : 3.187517 s : 3.187517
pz : 1.003739 p : 3.022563
px : 0.946297
py : 1.072526
1 C s : 3.187019 s : 3.187019
pz : 1.004005 p : 3.022417
px : 0.946208
py : 1.072204
2 C s : 3.137897 s : 3.137897
pz : 1.002440 p : 3.027784
px : 1.116755
py : 0.908589
3 C s : 3.136201 s : 3.136201
pz : 0.987198 p : 2.936870
px : 0.908565
py : 1.041107
4 C s : 3.137659 s : 3.137659
pz : 1.002543 p : 3.027603
px : 1.116657
py : 0.908403
5 C s : 3.187151 s : 3.187151
pz : 1.003982 p : 3.022485
px : 0.946037
py : 1.072466
6 C s : 3.187317 s : 3.187317
pz : 1.003774 p : 3.022499
px : 0.946485
py : 1.072240
7 C s : 3.137521 s : 3.137521
pz : 1.002784 p : 3.027843
px : 1.116543
py : 0.908516
8 C s : 3.136534 s : 3.136534
pz : 0.986715 p : 2.937185
px : 0.908725
py : 1.041745
9 C s : 3.137235 s : 3.137235
pz : 1.002820 p : 3.027610
px : 1.116530
py : 0.908259
10 H s : 0.798710 s : 0.798710
11 H s : 0.798294 s : 0.798294
12 H s : 0.789868 s : 0.789868
13 H s : 0.789861 s : 0.789861
14 H s : 0.798369 s : 0.798369
15 H s : 0.798563 s : 0.798563
16 H s : 0.789802 s : 0.789802
17 H s : 0.789623 s : 0.789623
*******************************
* LOEWDIN POPULATION ANALYSIS *
*******************************
----------------------
LOEWDIN ATOMIC CHARGES
----------------------
0 C : -0.124773
1 C : -0.124901
2 C : -0.111315
3 C : -0.023975
4 C : -0.111339
5 C : -0.124892
6 C : -0.124770
7 C : -0.111531
8 C : -0.023723
9 C : -0.111525
10 H : 0.124067
11 H : 0.124242
12 H : 0.123992
13 H : 0.123994
14 H : 0.124215
15 H : 0.124131
16 H : 0.124011
17 H : 0.124092
-------------------------------
LOEWDIN REDUCED ORBITAL CHARGES
-------------------------------
0 C s : 2.940758 s : 2.940758
pz : 1.003498 p : 3.184015
px : 1.077353
py : 1.103164
1 C s : 2.940814 s : 2.940814
pz : 1.003773 p : 3.184087
px : 1.077218
py : 1.103095
2 C s : 2.937356 s : 2.937356
pz : 1.004045 p : 3.173959
px : 1.101288
py : 1.068625
3 C s : 2.895924 s : 2.895924
pz : 0.984437 p : 3.128051
px : 1.073508
py : 1.070107
4 C s : 2.937396 s : 2.937396
pz : 1.004150 p : 3.173943
px : 1.101271
py : 1.068521
5 C s : 2.940804 s : 2.940804
pz : 1.003745 p : 3.184088
px : 1.077167
py : 1.103176
6 C s : 2.940767 s : 2.940767
pz : 1.003549 p : 3.184003
px : 1.077275
py : 1.103179
7 C s : 2.937265 s : 2.937265
pz : 1.004369 p : 3.174266
px : 1.101267
py : 1.068630
8 C s : 2.895998 s : 2.895998
pz : 0.984013 p : 3.127725
px : 1.073567
py : 1.070145
9 C s : 2.937292 s : 2.937292
pz : 1.004421 p : 3.174233
px : 1.101351
py : 1.068461
10 H s : 0.875933 s : 0.875933
11 H s : 0.875758 s : 0.875758
12 H s : 0.876008 s : 0.876008
13 H s : 0.876006 s : 0.876006
14 H s : 0.875785 s : 0.875785
15 H s : 0.875869 s : 0.875869
16 H s : 0.875989 s : 0.875989
17 H s : 0.875908 s : 0.875908
*****************************
* MAYER POPULATION ANALYSIS *
*****************************
NA - Mulliken gross atomic population
ZA - Total nuclear charge
QA - Mulliken gross atomic charge
VA - Mayer's total valence
BVA - Mayer's bonded valence
FA - Mayer's free valence
ATOM NA ZA QA VA BVA FA
0 C 6.2101 6.0000 -0.2101 3.8641 3.8641 0.0000
1 C 6.2094 6.0000 -0.2094 3.8637 3.8637 0.0000
2 C 6.1657 6.0000 -0.1657 3.8827 3.8827 -0.0000
3 C 6.0731 6.0000 -0.0731 3.8738 3.8738 -0.0000
4 C 6.1653 6.0000 -0.1653 3.8826 3.8826 0.0000
5 C 6.2096 6.0000 -0.2096 3.8639 3.8639 -0.0000
6 C 6.2098 6.0000 -0.2098 3.8640 3.8640 -0.0000
7 C 6.1654 6.0000 -0.1654 3.8826 3.8826 -0.0000
8 C 6.0737 6.0000 -0.0737 3.8742 3.8742 0.0000
9 C 6.1648 6.0000 -0.1648 3.8825 3.8825 0.0000
10 H 0.7987 1.0000 0.2013 0.9338 0.9338 0.0000
11 H 0.7983 1.0000 0.2017 0.9337 0.9337 -0.0000
12 H 0.7899 1.0000 0.2101 0.9288 0.9288 0.0000
13 H 0.7899 1.0000 0.2101 0.9288 0.9288 0.0000
14 H 0.7984 1.0000 0.2016 0.9337 0.9337 -0.0000
15 H 0.7986 1.0000 0.2014 0.9338 0.9338 0.0000
16 H 0.7898 1.0000 0.2102 0.9287 0.9287 -0.0000
17 H 0.7896 1.0000 0.2104 0.9287 0.9287 -0.0000
Mayer bond orders larger than 0.1
B( 0-C , 1-C ) : 1.2744 B( 0-C , 9-C ) : 1.6171 B( 0-C , 10-H ) : 0.9418
B( 1-C , 2-C ) : 1.6169 B( 1-C , 11-H ) : 0.9416 B( 2-C , 3-C ) : 1.2534
B( 2-C , 12-H ) : 0.9356 B( 3-C , 4-C ) : 1.2527 B( 3-C , 8-C ) : 1.3514
B( 4-C , 5-C ) : 1.6177 B( 4-C , 13-H ) : 0.9356 B( 5-C , 6-C ) : 1.2739
B( 5-C , 14-H ) : 0.9416 B( 6-C , 7-C ) : 1.6177 B( 6-C , 15-H ) : 0.9417
B( 7-C , 8-C ) : 1.2528 B( 7-C , 16-H ) : 0.9356 B( 8-C , 9-C ) : 1.2532
B( 9-C , 17-H ) : 0.9355
-------
TIMINGS
-------
Total SCF time: 0 days 0 hours 1 min 0 sec
Total time .... 60.935 sec
Sum of individual times .... 63.248 sec (103.8%)
Fock matrix formation .... 60.848 sec ( 99.9%)
Diagonalization .... 0.022 sec ( 0.0%)
Density matrix formation .... 0.004 sec ( 0.0%)
Population analysis .... 0.009 sec ( 0.0%)
Initial guess .... 1.660 sec ( 2.7%)
Orbital Transformation .... 0.000 sec ( 0.0%)
Orbital Orthonormalization .... 0.000 sec ( 0.0%)
DIIS solution .... 0.007 sec ( 0.0%)
SOSCF solution .... 0.024 sec ( 0.0%)
------------------------- --------------------
FINAL SINGLE POINT ENERGY -383.220154291480
------------------------- --------------------
------------------------------------------------------------------------------
ORCA SCF GRADIENT CALCULATION
------------------------------------------------------------------------------
Gradient of the Hartree-Fock SCF energy:
Hartree-Fock type ... RHF
Number of operators ... 1
Number of atoms ... 18
Basis set dimensions ... 106
Integral neglect threshold ... 2.5e-11
Integral primitive cutoff ... 2.5e-12
Nuclear repulsion gradient ... done
One Electron Gradient ... done
Pre-screening matrix ... done
Starting the two electron gradient:
Two electron gradient done
------------------
CARTESIAN GRADIENT
------------------
1 C : 0.001696057 0.001051372 0.000013410
2 C : -0.001494677 -0.000179347 -0.000032382
3 C : 0.001609669 0.002105412 0.000076382
4 C : -0.003008134 -0.000214954 -0.000067622
5 C : 0.001530848 -0.001648837 0.000025838
6 C : -0.001278488 -0.000072972 -0.000077788
7 C : 0.001376422 -0.000757189 0.000117827
8 C : -0.001565313 -0.001455422 -0.000071984
9 C : 0.003244839 0.000066305 0.000033040
10 C : -0.002138441 0.001342431 0.000004720
11 H : -0.004192198 -0.010869527 -0.000017748
12 H : 0.004211100 -0.010813166 0.000012928
13 H : 0.010964226 0.000741203 0.000021857
14 H : 0.011092462 -0.000785664 -0.000087459
15 H : 0.004143591 0.010762833 0.000022922
16 H : -0.004202509 0.010799727 0.000058719
17 H : -0.011051061 -0.000886694 -0.000036881
18 H : -0.010938395 0.000814489 0.000004221
Norm of the cartesian gradient ... 0.032838944
RMS gradient ... 0.004468814
MAX gradient ... 0.011092462
-------
TIMINGS
-------
Total SCF gradient time ... 17.279 sec
One electron gradient .... 0.298 sec ( 1.7%)
Prescreening matrices .... 0.092 sec ( 0.5%)
Two electron gradient .... 16.683 sec ( 96.6%)
------------------------------------------------------------------------------
ORCA GEOMETRY RELAXATION STEP
------------------------------------------------------------------------------
Reading the OPT-File .... done
Getting information on internals .... done
Copying old internal coords+grads .... done
Making the new internal coordinates .... (new redundants).... done
Validating the new internal coordinates .... (new redundants).... done
Calculating the B-matrix .... done
Calculating the G,G- and P matrices .... done
Transforming gradient to internals .... done
Projecting the internal gradient .... done
Number of atoms .... 18
Number of internal coordinates .... 93
Current Energy .... -383.220154291 Eh
Current gradient norm .... 0.032838944 Eh/bohr
Maximum allowed component of the step .... 0.300
Current trust radius .... 0.300
Evaluating the initial hessian .... (Almloef) done
Projecting the Hessian .... done
Forming the augmented Hessian .... done
Diagonalizing the augmented Hessian .... done
Last element of RFO vector .... 0.994364937
Lowest eigenvalues of augmented Hessian:
-0.004965439 0.020033141 0.020274322 0.020341775 0.023076712
Length of the computed step .... 0.106611956
The final length of the internal step .... 0.106611956
Converting the step to cartesian space:
Initial RMS(Int)= 0.0110551449
Transforming coordinates:
Iter 0: RMS(Cart)= 0.0243122706 RMS(Int)= 0.6515742969
Iter 1: RMS(Cart)= 0.0000513649 RMS(Int)= 0.0000264071
Iter 2: RMS(Cart)= 0.0000007586 RMS(Int)= 0.0000004176
Iter 3: RMS(Cart)= 0.0000000104 RMS(Int)= 0.0000000059
done
Storing new coordinates .... done
.--------------------.
----------------------|Geometry convergence|---------------------
Item value Tolerance Converged
-----------------------------------------------------------------
RMS gradient 0.00498796 0.00010000 NO
MAX gradient 0.01258056 0.00030000 NO
RMS step 0.01105514 0.00200000 NO
MAX step 0.03149843 0.00400000 NO
....................................................
Max(Bonds) 0.0167 Max(Angles) 0.31
Max(Dihed) 0.12 Max(Improp) 0.00
-----------------------------------------------------------------
The optimization has not yet converged - more geometry cycles are needed
---------------------------------------------------------------------------
Redundant Internal Coordinates
(Angstroem and degrees)
Definition Value dE/dq Step New-Value
----------------------------------------------------------------------------
1. B(C 1,C 0) 1.4259 0.009340 -0.0091 1.4168
2. B(C 2,C 1) 1.3723 0.012581 -0.0100 1.3623
3. B(C 3,C 2) 1.4310 0.009758 -0.0094 1.4216
4. B(C 4,C 3) 1.4315 0.010004 -0.0097 1.4218
5. B(C 5,C 4) 1.3720 0.012417 -0.0098 1.3622
6. B(C 6,C 5) 1.4262 0.009459 -0.0092 1.4169
7. B(C 7,C 6) 1.3717 0.012158 -0.0096 1.3621
8. B(C 8,C 7) 1.4312 0.009783 -0.0095 1.4218
9. B(C 8,C 3) 1.4195 0.008972 -0.0080 1.4114
10. B(C 9,C 8) 1.4314 0.009982 -0.0097 1.4218
11. B(C 9,C 0) 1.3718 0.012185 -0.0097 1.3622
12. B(H 10,C 0) 1.0888 0.011549 -0.0167 1.0721
13. B(H 11,C 1) 1.0886 0.011506 -0.0166 1.0720
14. B(H 12,C 2) 1.0887 0.010971 -0.0158 1.0729
15. B(H 13,C 4) 1.0889 0.011099 -0.0160 1.0729
16. B(H 14,C 5) 1.0886 0.011432 -0.0165 1.0721
17. B(H 15,C 6) 1.0887 0.011490 -0.0166 1.0721
18. B(H 16,C 7) 1.0888 0.011060 -0.0160 1.0729
19. B(H 17,C 9) 1.0886 0.010945 -0.0158 1.0729
20. A(C 9,C 0,H 10) 120.88 0.001312 -0.20 120.68
21. A(C 1,C 0,H 10) 118.65 -0.001842 0.31 118.96
22. A(C 1,C 0,C 9) 120.47 0.000530 -0.11 120.36
23. A(C 0,C 1,C 2) 120.34 0.000025 -0.04 120.30
24. A(C 2,C 1,H 11) 120.93 0.001535 -0.23 120.70
25. A(C 0,C 1,H 11) 118.73 -0.001559 0.27 118.99
26. A(C 1,C 2,C 3) 120.46 -0.001108 0.16 120.62
27. A(C 1,C 2,H 12) 120.88 0.001210 -0.18 120.69
28. A(C 3,C 2,H 12) 118.66 -0.000103 0.02 118.69
29. A(C 2,C 3,C 4) 121.69 -0.001776 0.20 121.88
30. A(C 2,C 3,C 8) 119.16 0.000904 -0.10 119.06
31. A(C 4,C 3,C 8) 119.15 0.000872 -0.10 119.05
32. A(C 5,C 4,H 13) 120.90 0.001266 -0.19 120.71
33. A(C 3,C 4,H 13) 118.63 -0.000157 0.03 118.66
34. A(C 3,C 4,C 5) 120.47 -0.001109 0.16 120.63
35. A(C 6,C 5,H 14) 118.71 -0.001605 0.27 118.98
36. A(C 4,C 5,H 14) 120.93 0.001529 -0.23 120.71
37. A(C 4,C 5,C 6) 120.36 0.000076 -0.04 120.31
38. A(C 7,C 6,H 15) 120.90 0.001373 -0.21 120.69
39. A(C 5,C 6,H 15) 118.68 -0.001732 0.29 118.97
40. A(C 5,C 6,C 7) 120.42 0.000358 -0.08 120.34
41. A(C 8,C 7,H 16) 118.61 -0.000234 0.04 118.65
42. A(C 6,C 7,H 16) 120.94 0.001358 -0.21 120.73
43. A(C 6,C 7,C 8) 120.45 -0.001124 0.17 120.62
44. A(C 7,C 8,C 9) 121.66 -0.001937 0.22 121.88
45. A(C 3,C 8,C 9) 119.18 0.001010 -0.11 119.06
46. A(C 3,C 8,C 7) 119.16 0.000927 -0.10 119.06
47. A(C 8,C 9,H 17) 118.66 -0.000062 0.02 118.68
48. A(C 0,C 9,H 17) 120.95 0.001424 -0.22 120.73
49. A(C 0,C 9,C 8) 120.39 -0.001362 0.20 120.59
50. D(H 11,C 1,C 0,H 10) -0.04 -0.000009 0.02 -0.02
51. D(C 2,C 1,C 0,C 9) -0.03 -0.000007 0.02 -0.01
52. D(H 11,C 1,C 0,C 9) 179.96 -0.000012 0.03 179.99
53. D(C 2,C 1,C 0,H 10) 179.98 -0.000004 0.01 179.99
54. D(C 3,C 2,C 1,C 0) -0.01 -0.000010 0.02 0.01
55. D(H 12,C 2,C 1,H 11) 0.00 0.000001 -0.00 -0.00
56. D(C 3,C 2,C 1,H 11) -180.00 -0.000005 0.01 -179.99
57. D(H 12,C 2,C 1,C 0) 179.98 -0.000004 0.01 179.99
58. D(C 8,C 3,C 2,H 12) -179.93 0.000021 -0.05 -179.98
59. D(C 4,C 3,C 2,H 12) 0.03 0.000010 -0.02 0.01
60. D(C 4,C 3,C 2,C 1) -179.98 0.000016 -0.03 -180.01
61. D(C 8,C 3,C 2,C 1) 0.06 0.000027 -0.06 0.00
62. D(H 13,C 4,C 3,C 2) 0.15 0.000045 -0.10 0.05
63. D(C 5,C 4,C 3,C 8) 0.09 0.000035 -0.07 0.02
64. D(C 5,C 4,C 3,C 2) -179.87 0.000046 -0.10 -179.97
65. D(H 13,C 4,C 3,C 8) -179.89 0.000034 -0.07 -179.96
66. D(H 14,C 5,C 4,H 13) -0.06 -0.000024 0.04 -0.02
67. D(H 14,C 5,C 4,C 3) 179.96 -0.000026 0.04 180.00
68. D(C 6,C 5,C 4,H 13) 179.95 -0.000004 0.01 179.97
69. D(C 6,C 5,C 4,C 3) -0.02 -0.000005 0.01 -0.01
70. D(H 15,C 6,C 5,H 14) -0.02 0.000003 -0.00 -0.03
71. D(H 15,C 6,C 5,C 4) 179.96 -0.000017 0.03 179.98
72. D(C 7,C 6,C 5,H 14) 179.93 -0.000025 0.06 179.99
73. D(C 7,C 6,C 5,C 4) -0.09 -0.000045 0.09 -0.00
74. D(H 16,C 7,C 6,H 15) 0.05 0.000010 -0.01 0.04
75. D(H 16,C 7,C 6,C 5) -179.90 0.000040 -0.07 -179.98
76. D(C 8,C 7,C 6,H 15) -179.92 0.000033 -0.06 -179.98
77. D(C 8,C 7,C 6,C 5) 0.13 0.000063 -0.12 0.01
78. D(C 9,C 8,C 3,C 2) -0.07 -0.000028 0.06 -0.01
79. D(C 7,C 8,C 3,C 4) -0.05 -0.000017 0.04 -0.02
80. D(C 7,C 8,C 3,C 2) 179.91 -0.000029 0.07 179.97
81. D(C 9,C 8,C 7,H 16) -0.05 -0.000011 0.02 -0.03
82. D(C 9,C 8,C 7,C 6) 179.93 -0.000033 0.06 179.99
83. D(C 3,C 8,C 7,H 16) 179.97 -0.000010 0.01 179.99
84. D(C 3,C 8,C 7,C 6) -0.06 -0.000032 0.06 0.00
85. D(C 9,C 8,C 3,C 4) 179.97 -0.000016 0.03 180.00
86. D(H 17,C 9,C 8,C 7) 0.05 0.000008 -0.03 0.02
87. D(C 0,C 9,C 8,C 7) -179.95 0.000011 -0.03 -179.98
88. D(C 0,C 9,C 8,C 3) 0.03 0.000010 -0.02 0.01
89. D(H 17,C 9,C 0,H 10) 0.02 0.000007 -0.01 0.01
90. D(H 17,C 9,C 0,C 1) -179.98 0.000010 -0.02 -180.00
91. D(H 17,C 9,C 8,C 3) -179.97 0.000008 -0.02 -179.99
92. D(C 8,C 9,C 0,H 10) -179.99 0.000004 -0.01 -180.00
93. D(C 8,C 9,C 0,C 1) 0.01 0.000007 -0.02 -0.00
----------------------------------------------------------------------------
*************************************************************
* GEOMETRY OPTIMIZATION CYCLE 2 *
*************************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C -0.052248 -0.020593 -0.036774
C 1.364531 -0.020013 -0.037548
C 2.051444 1.156419 -0.037609
C 1.360089 2.398565 -0.036747
C 2.049730 3.641896 -0.036664
C 1.361337 4.817301 -0.035188
C -0.055611 4.816192 -0.033990
C -0.742619 3.640064 -0.034322
C -0.051312 2.397668 -0.035736
C -0.741192 1.154503 -0.035896
H -0.570976 -0.958895 -0.036949
H 1.884533 -0.957500 -0.037990
H 3.124324 1.164178 -0.038074
H 3.122605 3.635250 -0.038121
H 1.880082 5.755508 -0.035085
H -0.575685 5.753712 -0.032566
H -1.815469 3.631809 -0.033767
H -1.814024 1.161046 -0.035244
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 -0.098733479797658 -0.038915561382531 -0.069491984977217
1 C 6.0000 0 12.011 2.578589794761612 -0.037819562485171 -0.070955541163103
2 C 6.0000 0 12.011 3.876668179793008 2.185315761533276 -0.071070611788642
3 C 6.0000 0 12.011 2.570195670930886 4.532630311872078 -0.069441129151293
4 C 6.0000 0 12.011 3.873428694815066 6.882186446392776 -0.069284627450152
5 C 6.0000 0 12.011 2.572553887832906 9.103379044753849 -0.066496265243751
6 C 6.0000 0 12.011 -0.105089969180226 9.101283093158170 -0.064232648677400
7 C 6.0000 0 12.011 -1.403345601081815 6.878723958841918 -0.064859726029489
8 C 6.0000 0 12.011 -0.096965995674478 4.530936542855200 -0.067530881603696
9 C 6.0000 0 12.011 -1.400650592314727 2.181694383694877 -0.067833870681690
10 H 1.0000 0 1.008 -1.078987912410004 -1.812048247606288 -0.069822859621986
11 H 1.0000 0 1.008 3.561250435943879 -1.809411930824439 -0.071791486760127
12 H 1.0000 0 1.008 5.904117421170696 2.199976666640510 -0.071949481238643
13 H 1.0000 0 1.008 5.900869005519506 6.869627316098091 -0.072037792821090
14 H 1.0000 0 1.008 3.552839779345730 10.876333231079032 -0.066300494694851
15 H 1.0000 0 1.008 -1.087886470840935 10.872939865589062 -0.061540895477189
16 H 1.0000 0 1.008 -3.430739676828470 6.863125280262270 -0.063810831396376
17 H 1.0000 0 1.008 -3.428008588414236 2.194059292380719 -0.066601632060434
--------------------------------
INTERNAL COORDINATES (ANGSTROEM)
--------------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 1.416779 0.000 0.000
C 2 1 0 1.362294 120.304 0.000
C 3 2 1 1.421583 120.620 0.000
C 4 3 2 1.421787 121.885 179.994
C 5 4 3 1.362154 120.628 180.031
C 6 5 4 1.416949 120.311 0.000
C 7 6 5 1.362078 120.335 0.000
C 4 3 2 1.411402 119.063 0.000
C 1 2 3 1.362166 120.359 0.000
H 1 2 3 1.072142 118.959 179.987
H 2 1 3 1.072046 118.993 179.994
H 3 2 1 1.072908 120.695 179.993
H 5 4 3 1.072897 118.661 0.052
H 6 5 4 1.072067 120.705 179.998
H 7 6 5 1.072111 118.974 179.983
H 8 7 6 1.072883 120.731 180.022
H 10 1 2 1.072852 120.732 180.004
---------------------------
INTERNAL COORDINATES (A.U.)
---------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 2.677324 0.000 0.000
C 2 1 0 2.574362 120.304 0.000
C 3 2 1 2.686403 120.620 0.000
C 4 3 2 2.686788 121.885 179.994
C 5 4 3 2.574098 120.628 180.031
C 6 5 4 2.677646 120.311 0.000
C 7 6 5 2.573954 120.335 0.000
C 4 3 2 2.667163 119.063 0.000
C 1 2 3 2.574121 120.359 0.000
H 1 2 3 2.026055 118.959 179.987
H 2 1 3 2.025873 118.993 179.994
H 3 2 1 2.027502 120.695 179.993
H 5 4 3 2.027481 118.661 0.052
H 6 5 4 2.025914 120.705 179.998
H 7 6 5 2.025997 118.974 179.983
H 8 7 6 2.027454 120.731 180.022
H 10 1 2 2.027396 120.732 180.004
Diagonalization of the overlap matrix:
Smallest eigenvalue ... 3.796e-04
Time for diagonalization ... 0.004 sec
Threshold for overlap eigenvalues ... 1.000e-08
Number of eigenvalues below threshold ... 0
Time for construction of square roots ... 0.002 sec
Total time needed ... 0.006 sec
--------------
SCF ITERATIONS
--------------
ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp
*** Starting incremental Fock matrix formation ***
0 -383.2220364057 0.000000000000 0.00150523 0.00014792 0.0063690 0.7000
*** Initiating the SOSCF procedure ***
*** Re-Reading the Fockian ***
*** Removing any level shift ***
ITER Energy Delta-E Grad Rot Max-DP RMS-DP
1 -383.22221558 -0.0001791753 0.000701 0.000701 0.003871 0.000382
*** Restarting incremental Fock matrix formation ***
2 -383.22264398 -0.0004283952 0.000892 0.000770 0.000801 0.000085
3 -383.22266066 -0.0000166843 0.000194 0.000204 0.000318 0.000025
4 -383.22266209 -0.0000014301 0.000029 0.000049 0.000060 0.000005
5 -383.22266213 -0.0000000385 0.000016 0.000034 0.000024 0.000002
**** Energy Check signals convergence ****
***Rediagonalizing the Fockian in SOSCF/NRSCF***
*****************************************************
* SUCCESS *
* SCF CONVERGED AFTER 6 CYCLES *
*****************************************************
Total Energy : -383.22266214 Eh -10428.01879 eV
Last Energy change ... -7.6094e-09 Tolerance : 1.0000e-08
Last MAX-Density change ... 7.1934e-06 Tolerance : 1.0000e-07
**** THE GBW FILE WAS UPDATED (orca.gbw) ****
**** DENSITY FILE WAS UPDATED (orca.scfp.tmp) ****
**** ENERGY FILE WAS UPDATED (orca.en.tmp) ****
Total SCF time: 0 days 0 hours 0 min 35 sec
------------------------- --------------------
FINAL SINGLE POINT ENERGY -383.222662136691
------------------------- --------------------
------------------------------------------------------------------------------
ORCA SCF GRADIENT CALCULATION
------------------------------------------------------------------------------
Gradient of the Hartree-Fock SCF energy:
Hartree-Fock type ... RHF
Number of operators ... 1
Number of atoms ... 18
Basis set dimensions ... 106
Integral neglect threshold ... 2.5e-11
Integral primitive cutoff ... 2.5e-12
Nuclear repulsion gradient ... done
One Electron Gradient ... done
Pre-screening matrix ... done
Starting the two electron gradient:
Two electron gradient done
------------------
CARTESIAN GRADIENT
------------------
1 C : -0.001254309 -0.000094821 0.000013101
2 C : 0.001397106 -0.000600071 -0.000003103
3 C : 0.002118992 -0.000459302 -0.000006042
4 C : -0.002257824 -0.000108723 -0.000005348
5 C : 0.002115599 0.000676446 0.000025254
6 C : 0.001493913 0.000440657 0.000015639
7 C : -0.001427607 0.000204594 -0.000040961
8 C : -0.002185391 0.000789584 0.000043303
9 C : 0.002371944 -0.000009489 -0.000020244
10 C : -0.002383734 -0.000770651 0.000001326
11 H : 0.001205447 0.000124283 -0.000008473
12 H : -0.001208981 0.000167854 0.000008038
13 H : -0.000756752 0.000402681 0.000009468
14 H : -0.000765985 -0.000447293 -0.000030365
15 H : -0.001214390 -0.000153654 -0.000000396
16 H : 0.001200342 -0.000138125 0.000020678
17 H : 0.000770849 -0.000486260 -0.000021000
18 H : 0.000780781 0.000462288 -0.000000876
Norm of the cartesian gradient ... 0.007038833
RMS gradient ... 0.000957864
MAX gradient ... 0.002383734
-------
TIMINGS
-------
Total SCF gradient time ... 17.508 sec
One electron gradient .... 0.283 sec ( 1.6%)
Prescreening matrices .... 0.091 sec ( 0.5%)
Two electron gradient .... 16.952 sec ( 96.8%)
------------------------------------------------------------------------------
ORCA GEOMETRY RELAXATION STEP
------------------------------------------------------------------------------
Reading the OPT-File .... done
Getting information on internals .... done
Copying old internal coords+grads .... done
Making the new internal coordinates .... (new redundants).... done
Validating the new internal coordinates .... (new redundants).... done
Calculating the B-matrix .... done
Calculating the G,G- and P matrices .... done
Transforming gradient to internals .... done
Projecting the internal gradient .... done
Number of atoms .... 18
Number of internal coordinates .... 93
Current Energy .... -383.222662137 Eh
Current gradient norm .... 0.007038833 Eh/bohr
Maximum allowed component of the step .... 0.300
Current trust radius .... 0.300
Updating the Hessian (BFGS) .... done
Forming the augmented Hessian .... done
Diagonalizing the augmented Hessian .... done
Last element of RFO vector .... 0.999921739
Lowest eigenvalues of augmented Hessian:
-0.000059361 0.020032933 0.020274325 0.020341474 0.023076530
Length of the computed step .... 0.012511607
The final length of the internal step .... 0.012511607
Converting the step to cartesian space:
Initial RMS(Int)= 0.0012973932
Transforming coordinates:
Iter 0: RMS(Cart)= 0.0020133060 RMS(Int)= 0.9213953878
Iter 1: RMS(Cart)= 0.0000041406 RMS(Int)= 0.0000024950
Iter 2: RMS(Cart)= 0.0000000097 RMS(Int)= 0.0000000058
done
Storing new coordinates .... done
.--------------------.
----------------------|Geometry convergence|---------------------
Item value Tolerance Converged
-----------------------------------------------------------------
Energy change -0.00250785 0.00000500 NO
RMS gradient 0.00050125 0.00010000 NO
MAX gradient 0.00120124 0.00030000 NO
RMS step 0.00129739 0.00200000 YES
MAX step 0.00344136 0.00400000 YES
....................................................
Max(Bonds) 0.0010 Max(Angles) 0.20
Max(Dihed) 0.04 Max(Improp) 0.00
-----------------------------------------------------------------
The optimization has not yet converged - more geometry cycles are needed
---------------------------------------------------------------------------
Redundant Internal Coordinates
(Angstroem and degrees)
Definition Value dE/dq Step New-Value
----------------------------------------------------------------------------
1. B(C 1,C 0) 1.4168 0.000632 -0.0007 1.4160
2. B(C 2,C 1) 1.3623 0.000482 -0.0005 1.3618
3. B(C 3,C 2) 1.4216 0.000757 -0.0009 1.4207
4. B(C 4,C 3) 1.4218 0.000850 -0.0009 1.4208
5. B(C 5,C 4) 1.3622 0.000413 -0.0005 1.3617
6. B(C 6,C 5) 1.4169 0.000704 -0.0008 1.4161
7. B(C 7,C 6) 1.3621 0.000347 -0.0004 1.3617
8. B(C 8,C 7) 1.4218 0.000829 -0.0009 1.4209
9. B(C 8,C 3) 1.4114 -0.000415 0.0003 1.4117
10. B(C 9,C 8) 1.4218 0.000855 -0.0010 1.4208
11. B(C 9,C 0) 1.3622 0.000385 -0.0004 1.3617
12. B(H 10,C 0) 1.0721 -0.000692 0.0008 1.0730
13. B(H 11,C 1) 1.0720 -0.000733 0.0009 1.0729
14. B(H 12,C 2) 1.0729 -0.000754 0.0009 1.0738
15. B(H 13,C 4) 1.0729 -0.000763 0.0009 1.0738
16. B(H 14,C 5) 1.0721 -0.000722 0.0009 1.0729
17. B(H 15,C 6) 1.0721 -0.000703 0.0008 1.0729
18. B(H 16,C 7) 1.0729 -0.000767 0.0009 1.0738
19. B(H 17,C 9) 1.0729 -0.000778 0.0009 1.0738
20. A(C 9,C 0,H 10) 120.68 0.000814 -0.14 120.54
21. A(C 1,C 0,H 10) 118.96 -0.001201 0.20 119.16
22. A(C 1,C 0,C 9) 120.36 0.000387 -0.06 120.30
23. A(C 0,C 1,C 2) 120.30 0.000161 -0.03 120.28
24. A(C 2,C 1,H 11) 120.70 0.000908 -0.15 120.55
25. A(C 0,C 1,H 11) 118.99 -0.001069 0.18 119.17
26. A(C 1,C 2,C 3) 120.62 -0.000622 0.09 120.71
27. A(C 1,C 2,H 12) 120.69 0.000725 -0.11 120.58
28. A(C 3,C 2,H 12) 118.69 -0.000103 0.02 118.71
29. A(C 2,C 3,C 4) 121.88 -0.000768 0.10 121.99
30. A(C 2,C 3,C 8) 119.06 0.000403 -0.05 119.01
31. A(C 4,C 3,C 8) 119.05 0.000364 -0.05 119.00
32. A(C 5,C 4,H 13) 120.71 0.000759 -0.12 120.59
33. A(C 3,C 4,H 13) 118.66 -0.000158 0.03 118.69
34. A(C 3,C 4,C 5) 120.63 -0.000601 0.09 120.71
35. A(C 6,C 5,H 14) 118.98 -0.001096 0.18 119.17
36. A(C 4,C 5,H 14) 120.71 0.000906 -0.15 120.55
37. A(C 4,C 5,C 6) 120.31 0.000190 -0.03 120.28
38. A(C 7,C 6,H 15) 120.69 0.000848 -0.14 120.55
39. A(C 5,C 6,H 15) 118.97 -0.001143 0.19 119.16
40. A(C 5,C 6,C 7) 120.34 0.000295 -0.05 120.29
41. A(C 8,C 7,H 16) 118.65 -0.000181 0.04 118.69
42. A(C 6,C 7,H 16) 120.73 0.000817 -0.13 120.60
43. A(C 6,C 7,C 8) 120.62 -0.000636 0.09 120.71
44. A(C 7,C 8,C 9) 121.88 -0.000802 0.11 121.99
45. A(C 3,C 8,C 9) 119.06 0.000414 -0.06 119.01
46. A(C 3,C 8,C 7) 119.06 0.000387 -0.05 119.00
47. A(C 8,C 9,H 17) 118.68 -0.000102 0.02 118.70
48. A(C 0,C 9,H 17) 120.73 0.000845 -0.13 120.60
49. A(C 0,C 9,C 8) 120.59 -0.000743 0.11 120.70
50. D(H 11,C 1,C 0,H 10) -0.02 -0.000006 0.01 -0.00
51. D(C 2,C 1,C 0,C 9) -0.01 -0.000003 0.01 -0.00
52. D(H 11,C 1,C 0,C 9) 179.99 -0.000004 0.01 180.00
53. D(C 2,C 1,C 0,H 10) 179.99 -0.000004 0.01 180.00
54. D(C 3,C 2,C 1,C 0) 0.01 0.000003 -0.01 0.00
55. D(H 12,C 2,C 1,H 11) -0.00 -0.000002 0.00 0.00
56. D(C 3,C 2,C 1,H 11) -179.99 0.000005 -0.01 -180.00
57. D(H 12,C 2,C 1,C 0) 179.99 -0.000004 0.01 180.00
58. D(C 8,C 3,C 2,H 12) -179.98 0.000006 -0.02 -180.00
59. D(C 4,C 3,C 2,H 12) 0.01 0.000004 -0.01 -0.00
60. D(C 4,C 3,C 2,C 1) 179.99 -0.000002 0.01 180.00
61. D(C 8,C 3,C 2,C 1) 0.00 0.000000 -0.00 0.00
62. D(H 13,C 4,C 3,C 2) 0.05 0.000017 -0.04 0.01
63. D(C 5,C 4,C 3,C 8) 0.02 0.000006 -0.02 0.00
64. D(C 5,C 4,C 3,C 2) -179.97 0.000008 -0.03 -179.99
65. D(H 13,C 4,C 3,C 8) -179.96 0.000015 -0.04 -179.99
66. D(H 14,C 5,C 4,H 13) -0.02 -0.000009 0.02 -0.00
67. D(H 14,C 5,C 4,C 3) 180.00 -0.000000 -0.00 180.00
68. D(C 6,C 5,C 4,H 13) 179.97 -0.000014 0.03 180.00
69. D(C 6,C 5,C 4,C 3) -0.01 -0.000005 0.01 -0.00
70. D(H 15,C 6,C 5,H 14) -0.03 -0.000010 0.02 -0.00
71. D(H 15,C 6,C 5,C 4) 179.98 -0.000006 0.01 180.00
72. D(C 7,C 6,C 5,H 14) 179.99 -0.000002 0.01 180.00
73. D(C 7,C 6,C 5,C 4) -0.00 0.000003 -0.00 -0.00
74. D(H 16,C 7,C 6,H 15) 0.04 0.000015 -0.03 0.01
75. D(H 16,C 7,C 6,C 5) -179.98 0.000006 -0.02 -179.99
76. D(C 8,C 7,C 6,H 15) -179.98 0.000007 -0.02 -179.99
77. D(C 8,C 7,C 6,C 5) 0.01 -0.000001 0.00 0.01
78. D(C 9,C 8,C 3,C 2) -0.01 -0.000003 0.01 -0.00
79. D(C 7,C 8,C 3,C 4) -0.02 -0.000005 0.01 -0.00
80. D(C 7,C 8,C 3,C 2) 179.97 -0.000007 0.02 180.00
81. D(C 9,C 8,C 7,H 16) -0.03 -0.000009 0.02 -0.00
82. D(C 9,C 8,C 7,C 6) 179.99 -0.000001 0.01 179.99
83. D(C 3,C 8,C 7,H 16) 179.99 -0.000005 0.01 180.00
84. D(C 3,C 8,C 7,C 6) 0.00 0.000002 -0.01 -0.00
85. D(C 9,C 8,C 3,C 4) 180.00 -0.000001 0.00 180.00
86. D(H 17,C 9,C 8,C 7) 0.02 0.000005 -0.02 0.00
87. D(C 0,C 9,C 8,C 7) -179.98 0.000007 -0.02 -180.00
88. D(C 0,C 9,C 8,C 3) 0.01 0.000004 -0.01 0.00
89. D(H 17,C 9,C 0,H 10) 0.01 0.000003 -0.01 0.00
90. D(H 17,C 9,C 0,C 1) -180.00 0.000002 -0.00 -180.00
91. D(H 17,C 9,C 8,C 3) -179.99 0.000001 -0.01 -180.00
92. D(C 8,C 9,C 0,H 10) -180.00 0.000001 -0.00 -180.00
93. D(C 8,C 9,C 0,C 1) -0.00 -0.000001 0.00 0.00
----------------------------------------------------------------------------
*************************************************************
* GEOMETRY OPTIMIZATION CYCLE 3 *
*************************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C -0.051933 -0.020681 -0.036745
C 1.364112 -0.019872 -0.037728
C 2.050025 1.156555 -0.037653
C 1.360253 2.398606 -0.036569
C 2.048328 3.641719 -0.036456
C 1.360901 4.817165 -0.035279
C -0.055243 4.816175 -0.034180
C -0.741206 3.639894 -0.034390
C -0.051467 2.397682 -0.035547
C -0.739631 1.154652 -0.035681
H -0.574129 -0.957983 -0.036860
H 1.887589 -0.956418 -0.038512
H 3.123823 1.162883 -0.038418
H 3.122134 3.636617 -0.037323
H 1.883111 5.754426 -0.035136
H -0.578718 5.752747 -0.033192
H -1.814995 3.633266 -0.033663
H -1.813415 1.159677 -0.034938
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 -0.098138834403975 -0.039081596323870 -0.069437664753803
1 C 6.0000 0 12.011 2.577798347751496 -0.037553300462906 -0.071295936089279
2 C 6.0000 0 12.011 3.873986492322457 2.185572454809287 -0.071154079440477
3 C 6.0000 0 12.011 2.570505769313286 4.532707772080851 -0.069106297553288
4 C 6.0000 0 12.011 3.870779828893218 6.881852460836398 -0.068891669474341
5 C 6.0000 0 12.011 2.571730034361045 9.103123402954814 -0.066667202554563
6 C 6.0000 0 12.011 -0.104394379177570 9.101251323406480 -0.064590485185846
7 C 6.0000 0 12.011 -1.400676714652142 6.878403520911437 -0.064987388100974
8 C 6.0000 0 12.011 -0.097258531708792 4.530961524853663 -0.067173607268124
9 C 6.0000 0 12.011 -1.397699694207893 2.181976027081361 -0.067428187330461
10 H 1.0000 0 1.008 -1.084946273201015 -1.810325661512986 -0.069655980967035
11 H 1.0000 0 1.008 3.567025974018720 -1.807368809805743 -0.072777178170537
12 H 1.0000 0 1.008 5.903170904757275 2.197531022090295 -0.072598591535749
13 H 1.0000 0 1.008 5.899977766415913 6.872210984789727 -0.070531027663361
14 H 1.0000 0 1.008 3.558564098316816 10.874288880557028 -0.066397983249609
15 H 1.0000 0 1.008 -1.093618630784535 10.871115810347092 -0.062723210354081
16 H 1.0000 0 1.008 -3.429844049928067 6.865877574009038 -0.063612977277826
17 H 1.0000 0 1.008 -3.426857524515494 2.191472502231433 -0.066023293867776
--------------------------------
INTERNAL COORDINATES (ANGSTROEM)
--------------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 1.416046 0.000 0.000
C 2 1 0 1.361785 120.277 0.000
C 3 2 1 1.420731 120.710 0.000
C 4 3 2 1.420838 121.989 180.000
C 5 4 3 1.361702 120.715 180.006
C 6 5 4 1.416145 120.280 0.000
C 7 6 5 1.361683 120.289 0.000
C 4 3 2 1.411721 119.008 0.000
C 1 2 3 1.361741 120.300 0.000
H 1 2 3 1.072951 119.156 179.998
H 2 1 3 1.072915 119.170 179.999
H 3 2 1 1.073817 120.582 180.001
H 5 4 3 1.073818 118.693 0.000
H 6 5 4 1.072921 120.555 179.996
H 7 6 5 1.072937 119.162 179.996
H 8 7 6 1.073810 120.603 180.006
H 10 1 2 1.073796 120.600 180.000
---------------------------
INTERNAL COORDINATES (A.U.)
---------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 2.675938 0.000 0.000
C 2 1 0 2.573401 120.277 0.000
C 3 2 1 2.684792 120.710 0.000
C 4 3 2 2.684994 121.989 180.000
C 5 4 3 2.573243 120.715 180.006
C 6 5 4 2.676126 120.280 0.000
C 7 6 5 2.573208 120.289 0.000
C 4 3 2 2.667766 119.008 0.000
C 1 2 3 2.573317 120.300 0.000
H 1 2 3 2.027583 119.156 179.998
H 2 1 3 2.027516 119.170 179.999
H 3 2 1 2.029220 120.582 180.001
H 5 4 3 2.029222 118.693 0.000
H 6 5 4 2.027528 120.555 179.996
H 7 6 5 2.027557 119.162 179.996
H 8 7 6 2.029206 120.603 180.006
H 10 1 2 2.029181 120.600 180.000
Diagonalization of the overlap matrix:
Smallest eigenvalue ... 3.773e-04
Time for diagonalization ... 0.004 sec
Threshold for overlap eigenvalues ... 1.000e-08
Number of eigenvalues below threshold ... 0
Time for construction of square roots ... 0.002 sec
Total time needed ... 0.006 sec
--------------
SCF ITERATIONS
--------------
ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp
*** Starting incremental Fock matrix formation ***
*** Initiating the SOSCF procedure ***
*** Re-Reading the Fockian ***
*** Removing any level shift ***
ITER Energy Delta-E Grad Rot Max-DP RMS-DP
0 -383.22269775 -383.2226977506 0.000338 0.000338 0.000556 0.000054
*** Restarting incremental Fock matrix formation ***
1 -383.22270374 -0.0000059861 0.000139 0.000146 0.000250 0.000019
2 -383.22270472 -0.0000009823 0.000059 0.000121 0.000126 0.000010
3 -383.22270483 -0.0000001132 0.000025 0.000048 0.000028 0.000002
4 -383.22270484 -0.0000000071 0.000012 0.000013 0.000007 0.000001
5 -383.22270484 -0.0000000024 0.000003 0.000008 0.000005 0.000000
***Gradient check signals convergence***
***Rediagonalizing the Fockian in SOSCF/NRSCF***
*****************************************************
* SUCCESS *
* SCF CONVERGED AFTER 6 CYCLES *
*****************************************************
Total Energy : -383.22270484 Eh -10428.01995 eV
Last Energy change ... -1.2797e-09 Tolerance : 1.0000e-08
Last MAX-Density change ... 2.1926e-06 Tolerance : 1.0000e-07
**** THE GBW FILE WAS UPDATED (orca.gbw) ****
**** DENSITY FILE WAS UPDATED (orca.scfp.tmp) ****
**** ENERGY FILE WAS UPDATED (orca.en.tmp) ****
Total SCF time: 0 days 0 hours 0 min 33 sec
------------------------- --------------------
FINAL SINGLE POINT ENERGY -383.222704843048
------------------------- --------------------
------------------------------------------------------------------------------
ORCA SCF GRADIENT CALCULATION
------------------------------------------------------------------------------
Gradient of the Hartree-Fock SCF energy:
Hartree-Fock type ... RHF
Number of operators ... 1
Number of atoms ... 18
Basis set dimensions ... 106
Integral neglect threshold ... 2.5e-11
Integral primitive cutoff ... 2.5e-12
Nuclear repulsion gradient ... done
One Electron Gradient ... done
Pre-screening matrix ... done
Starting the two electron gradient:
Two electron gradient done
------------------
CARTESIAN GRADIENT
------------------
1 C : -0.000661473 0.000655344 0.000001436
2 C : 0.000725864 0.000457032 -0.000002000
3 C : 0.000396062 -0.000520895 0.000002372
4 C : -0.001290978 -0.000055484 0.000000144
5 C : 0.000379599 0.000639539 0.000001785
6 C : 0.000785873 -0.000535392 -0.000007361
7 C : -0.000748356 -0.000614870 0.000004678
8 C : -0.000425839 0.000698166 -0.000002730
9 C : 0.001337115 -0.000021464 0.000000931
10 C : -0.000504099 -0.000656501 0.000002634
11 H : 0.000575936 -0.000255693 -0.000001974
12 H : -0.000574906 -0.000240142 0.000002406
13 H : -0.000111660 0.000262973 -0.000000712
14 H : -0.000111796 -0.000291390 -0.000002861
15 H : -0.000579633 0.000244873 0.000002265
16 H : 0.000573587 0.000249456 0.000003797
17 H : 0.000115062 -0.000311965 -0.000003985
18 H : 0.000119640 0.000296414 -0.000000825
Norm of the cartesian gradient ... 0.003347045
RMS gradient ... 0.000455475
MAX gradient ... 0.001337115
-------
TIMINGS
-------
Total SCF gradient time ... 17.450 sec
One electron gradient .... 0.282 sec ( 1.6%)
Prescreening matrices .... 0.093 sec ( 0.5%)
Two electron gradient .... 16.897 sec ( 96.8%)
------------------------------------------------------------------------------
ORCA GEOMETRY RELAXATION STEP
------------------------------------------------------------------------------
Reading the OPT-File .... done
Getting information on internals .... done
Copying old internal coords+grads .... done
Making the new internal coordinates .... (new redundants).... done
Validating the new internal coordinates .... (new redundants).... done
Calculating the B-matrix .... done
Calculating the G,G- and P matrices .... done
Transforming gradient to internals .... done
Projecting the internal gradient .... done
Number of atoms .... 18
Number of internal coordinates .... 93
Current Energy .... -383.222704843 Eh
Current gradient norm .... 0.003347045 Eh/bohr
Maximum allowed component of the step .... 0.300
Current trust radius .... 0.300
Updating the Hessian (BFGS) .... done
Forming the augmented Hessian .... done
Diagonalizing the augmented Hessian .... done
Last element of RFO vector .... 0.999898360
Lowest eigenvalues of augmented Hessian:
-0.000034186 0.020032551 0.020274366 0.020341666 0.023075424
Length of the computed step .... 0.014258725
The final length of the internal step .... 0.014258725
Converting the step to cartesian space:
Initial RMS(Int)= 0.0014785609
Transforming coordinates:
Iter 0: RMS(Cart)= 0.0025556847 RMS(Int)= 2.8399108116
Iter 1: RMS(Cart)= 0.0000059841 RMS(Int)= 0.0000040576
Iter 2: RMS(Cart)= 0.0000000224 RMS(Int)= 0.0000000120
done
Storing new coordinates .... done
.--------------------.
----------------------|Geometry convergence|---------------------
Item value Tolerance Converged
-----------------------------------------------------------------
Energy change -0.00004271 0.00000500 NO
RMS gradient 0.00025553 0.00010000 NO
MAX gradient 0.00073019 0.00030000 NO
RMS step 0.00147856 0.00200000 YES
MAX step 0.00451141 0.00400000 NO
....................................................
Max(Bonds) 0.0011 Max(Angles) 0.26
Max(Dihed) 0.02 Max(Improp) 0.00
-----------------------------------------------------------------
The optimization has not yet converged - more geometry cycles are needed
---------------------------------------------------------------------------
Redundant Internal Coordinates
(Angstroem and degrees)
Definition Value dE/dq Step New-Value
----------------------------------------------------------------------------
1. B(C 1,C 0) 1.4160 0.000107 -0.0004 1.4156
2. B(C 2,C 1) 1.3618 -0.000257 0.0002 1.3619
3. B(C 3,C 2) 1.4207 0.000147 -0.0005 1.4202
4. B(C 4,C 3) 1.4208 0.000190 -0.0006 1.4202
5. B(C 5,C 4) 1.3617 -0.000297 0.0002 1.3619
6. B(C 6,C 5) 1.4161 0.000149 -0.0005 1.4156
7. B(C 7,C 6) 1.3617 -0.000311 0.0003 1.3619
8. B(C 8,C 7) 1.4209 0.000199 -0.0007 1.4202
9. B(C 8,C 3) 1.4117 -0.000638 0.0011 1.4128
10. B(C 9,C 8) 1.4208 0.000189 -0.0006 1.4202
11. B(C 9,C 0) 1.3617 -0.000286 0.0002 1.3620
12. B(H 10,C 0) 1.0730 -0.000057 0.0002 1.0731
13. B(H 11,C 1) 1.0729 -0.000071 0.0002 1.0731
14. B(H 12,C 2) 1.0738 -0.000110 0.0004 1.0742
15. B(H 13,C 4) 1.0738 -0.000110 0.0004 1.0742
16. B(H 14,C 5) 1.0729 -0.000068 0.0002 1.0731
17. B(H 15,C 6) 1.0729 -0.000062 0.0002 1.0731
18. B(H 16,C 7) 1.0738 -0.000113 0.0004 1.0742
19. B(H 17,C 9) 1.0738 -0.000118 0.0004 1.0742
20. A(C 9,C 0,H 10) 120.54 0.000542 -0.19 120.35
21. A(C 1,C 0,H 10) 119.16 -0.000730 0.26 119.41
22. A(C 1,C 0,C 9) 120.30 0.000188 -0.06 120.24
23. A(C 0,C 1,C 2) 120.28 0.000095 -0.03 120.24
24. A(C 2,C 1,H 11) 120.55 0.000580 -0.21 120.35
25. A(C 0,C 1,H 11) 119.17 -0.000675 0.24 119.41
26. A(C 1,C 2,C 3) 120.71 -0.000316 0.10 120.81
27. A(C 1,C 2,H 12) 120.58 0.000425 -0.14 120.44
28. A(C 3,C 2,H 12) 118.71 -0.000110 0.04 118.75
29. A(C 2,C 3,C 4) 121.99 -0.000381 0.12 122.11
30. A(C 2,C 3,C 8) 119.01 0.000201 -0.06 118.95
31. A(C 4,C 3,C 8) 119.00 0.000180 -0.06 118.95
32. A(C 5,C 4,H 13) 120.59 0.000446 -0.15 120.44
33. A(C 3,C 4,H 13) 118.69 -0.000146 0.06 118.75
34. A(C 3,C 4,C 5) 120.71 -0.000301 0.10 120.81
35. A(C 6,C 5,H 14) 119.17 -0.000689 0.24 119.41
36. A(C 4,C 5,H 14) 120.55 0.000580 -0.21 120.35
37. A(C 4,C 5,C 6) 120.28 0.000109 -0.04 120.24
38. A(C 7,C 6,H 15) 120.55 0.000557 -0.20 120.35
39. A(C 5,C 6,H 15) 119.16 -0.000705 0.25 119.41
40. A(C 5,C 6,C 7) 120.29 0.000147 -0.05 120.24
41. A(C 8,C 7,H 16) 118.69 -0.000156 0.06 118.75
42. A(C 6,C 7,H 16) 120.60 0.000478 -0.16 120.44
43. A(C 6,C 7,C 8) 120.71 -0.000322 0.10 120.81
44. A(C 7,C 8,C 9) 121.99 -0.000385 0.12 122.11
45. A(C 3,C 8,C 9) 119.01 0.000198 -0.06 118.94
46. A(C 3,C 8,C 7) 119.00 0.000186 -0.06 118.94
47. A(C 8,C 9,H 17) 118.70 -0.000118 0.05 118.75
48. A(C 0,C 9,H 17) 120.60 0.000484 -0.17 120.43
49. A(C 0,C 9,C 8) 120.70 -0.000366 0.12 120.82
50. D(H 11,C 1,C 0,H 10) -0.00 -0.000001 0.01 0.01
51. D(C 2,C 1,C 0,C 9) -0.00 -0.000001 0.00 0.00
52. D(H 11,C 1,C 0,C 9) 180.00 -0.000001 0.01 180.00
53. D(C 2,C 1,C 0,H 10) 180.00 -0.000001 0.01 180.00
54. D(C 3,C 2,C 1,C 0) 0.00 0.000000 -0.00 -0.00
55. D(H 12,C 2,C 1,H 11) 0.00 0.000001 -0.00 -0.00
56. D(C 3,C 2,C 1,H 11) -180.00 0.000001 -0.00 -180.00
57. D(H 12,C 2,C 1,C 0) -180.00 0.000001 -0.00 -180.00
58. D(C 8,C 3,C 2,H 12) -180.00 0.000000 -0.01 -180.00
59. D(C 4,C 3,C 2,H 12) -0.00 -0.000000 -0.00 -0.00
60. D(C 4,C 3,C 2,C 1) 180.00 0.000000 0.00 180.00
61. D(C 8,C 3,C 2,C 1) 0.00 0.000000 -0.00 -0.00
62. D(H 13,C 4,C 3,C 2) 0.01 0.000002 -0.02 -0.01
63. D(C 5,C 4,C 3,C 8) 0.00 0.000002 -0.01 -0.01
64. D(C 5,C 4,C 3,C 2) -179.99 0.000002 -0.02 -180.01
65. D(H 13,C 4,C 3,C 8) -179.99 0.000002 -0.02 -180.01
66. D(H 14,C 5,C 4,H 13) -0.00 -0.000002 0.01 0.01
67. D(H 14,C 5,C 4,C 3) 180.00 -0.000002 0.01 180.00
68. D(C 6,C 5,C 4,H 13) 180.00 0.000000 0.01 180.01
69. D(C 6,C 5,C 4,C 3) -0.00 -0.000000 0.00 0.00
70. D(H 15,C 6,C 5,H 14) -0.00 -0.000000 0.01 0.00
71. D(H 15,C 6,C 5,C 4) 180.00 -0.000002 0.01 180.01
72. D(C 7,C 6,C 5,H 14) 180.00 -0.000001 0.01 180.00
73. D(C 7,C 6,C 5,C 4) -0.00 -0.000003 0.01 0.01
74. D(H 16,C 7,C 6,H 15) 0.01 0.000002 -0.01 -0.01
75. D(H 16,C 7,C 6,C 5) -179.99 0.000003 -0.01 -180.01
76. D(C 8,C 7,C 6,H 15) -179.99 0.000003 -0.02 -180.01
77. D(C 8,C 7,C 6,C 5) 0.01 0.000004 -0.02 -0.01
78. D(C 9,C 8,C 3,C 2) -0.00 -0.000001 0.01 0.00
79. D(C 7,C 8,C 3,C 4) -0.00 -0.000001 0.01 0.00
80. D(C 7,C 8,C 3,C 2) 180.00 -0.000001 0.01 180.01
81. D(C 9,C 8,C 7,H 16) -0.00 -0.000001 0.01 0.01
82. D(C 9,C 8,C 7,C 6) 179.99 -0.000002 0.01 180.01
83. D(C 3,C 8,C 7,H 16) 180.00 -0.000001 0.01 180.00
84. D(C 3,C 8,C 7,C 6) -0.00 -0.000002 0.01 0.00
85. D(C 9,C 8,C 3,C 4) 180.00 -0.000001 0.00 180.00
86. D(H 17,C 9,C 8,C 7) 0.00 0.000001 -0.01 -0.01
87. D(C 0,C 9,C 8,C 7) -180.00 0.000000 -0.01 -180.01
88. D(C 0,C 9,C 8,C 3) 0.00 0.000000 -0.00 -0.00
89. D(H 17,C 9,C 0,H 10) 0.00 0.000000 -0.00 -0.00
90. D(H 17,C 9,C 0,C 1) 180.00 -0.000000 -0.00 180.00
91. D(H 17,C 9,C 8,C 3) -180.00 0.000001 -0.01 -180.00
92. D(C 8,C 9,C 0,H 10) -180.00 0.000000 -0.00 -180.00
93. D(C 8,C 9,C 0,C 1) 0.00 0.000000 -0.00 -0.00
----------------------------------------------------------------------------
*************************************************************
* GEOMETRY OPTIMIZATION CYCLE 4 *
*************************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C -0.051777 -0.021721 -0.036746
C 1.363826 -0.020708 -0.037858
C 2.048984 1.156334 -0.037706
C 1.360815 2.398652 -0.036465
C 2.047322 3.641894 -0.036269
C 1.360598 4.818009 -0.035273
C -0.055015 4.817097 -0.034357
C -0.740148 3.640035 -0.034343
C -0.051979 2.397698 -0.035437
C -0.738442 1.154464 -0.035581
H -0.578150 -0.956893 -0.036819
H 1.891455 -0.955189 -0.038843
H 3.123144 1.160705 -0.038568
H 3.121490 3.638911 -0.036873
H 1.886952 5.753206 -0.035193
H -0.582608 5.751587 -0.033671
H -1.814312 3.635604 -0.033516
H -1.812616 1.157426 -0.034752
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 -0.097844022431691 -0.041047330950119 -0.069440348621850
1 C 6.0000 0 12.011 2.577256971936359 -0.039132604936795 -0.071541970772828
2 C 6.0000 0 12.011 3.872018382065127 2.185154854023675 -0.071254904384660
3 C 6.0000 0 12.011 2.571568220418011 4.532795331275765 -0.068908319080375
4 C 6.0000 0 12.011 3.868878708541504 6.882182996549052 -0.068538789836113
5 C 6.0000 0 12.011 2.571157854497377 9.104717457106130 -0.066657044128210
6 C 6.0000 0 12.011 -0.103963750853965 9.102994519708451 -0.064924378286378
7 C 6.0000 0 12.011 -1.398677098774683 6.878669230292600 -0.064898334747571
8 C 6.0000 0 12.011 -0.098225483892877 4.530992471347884 -0.066965573045401
9 C 6.0000 0 12.011 -1.395453120900061 2.181620490698656 -0.067238186658736
10 H 1.0000 0 1.008 -1.092545631723032 -1.808266627481927 -0.069577532168519
11 H 1.0000 0 1.008 3.574331882176200 -1.805046059178450 -0.073402371014929
12 H 1.0000 0 1.008 5.901887212282105 2.193414973662710 -0.072882058340843
13 H 1.0000 0 1.008 5.898761909846634 6.876545090892422 -0.069680375178595
14 H 1.0000 0 1.008 3.565822165378183 10.871983773640437 -0.066505999369572
15 H 1.0000 0 1.008 -1.100969271733728 10.868923906040729 -0.063628344794953
16 H 1.0000 0 1.008 -3.428552631155109 6.870295243926275 -0.063335754461140
17 H 1.0000 0 1.008 -3.425347712105613 2.187218176235902 -0.065672475946457
--------------------------------
INTERNAL COORDINATES (ANGSTROEM)
--------------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 1.415603 0.000 0.000
C 2 1 0 1.361936 120.245 0.000
C 3 2 1 1.420187 120.812 0.000
C 4 3 2 1.420191 122.109 180.000
C 5 4 3 1.361924 120.813 179.990
C 6 5 4 1.415614 120.243 0.000
C 7 6 5 1.361941 120.239 0.000
C 4 3 2 1.412795 118.945 0.000
C 1 2 3 1.361955 120.236 0.000
H 1 2 3 1.073134 119.415 180.004
H 2 1 3 1.073149 119.409 180.001
H 3 2 1 1.074170 120.437 180.001
H 5 4 3 1.074172 118.748 0.000
H 6 5 4 1.073146 120.348 180.004
H 7 6 5 1.073138 119.411 180.006
H 8 7 6 1.074173 120.439 179.992
H 10 1 2 1.074178 120.435 179.999
---------------------------
INTERNAL COORDINATES (A.U.)
---------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 2.675103 0.000 0.000
C 2 1 0 2.573686 120.245 0.000
C 3 2 1 2.683765 120.812 0.000
C 4 3 2 2.683773 122.109 180.000
C 5 4 3 2.573663 120.813 179.990
C 6 5 4 2.675123 120.243 0.000
C 7 6 5 2.573695 120.239 0.000
C 4 3 2 2.669795 118.945 0.000
C 1 2 3 2.573722 120.236 0.000
H 1 2 3 2.027929 119.415 180.004
H 2 1 3 2.027958 119.409 180.001
H 3 2 1 2.029886 120.437 180.001
H 5 4 3 2.029891 118.748 0.000
H 6 5 4 2.027952 120.348 180.004
H 7 6 5 2.027937 119.411 180.006
H 8 7 6 2.029893 120.439 179.992
H 10 1 2 2.029903 120.435 179.999
Diagonalization of the overlap matrix:
Smallest eigenvalue ... 3.762e-04
Time for diagonalization ... 0.004 sec
Threshold for overlap eigenvalues ... 1.000e-08
Number of eigenvalues below threshold ... 0
Time for construction of square roots ... 0.002 sec
Total time needed ... 0.006 sec
--------------
SCF ITERATIONS
--------------
ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp
*** Starting incremental Fock matrix formation ***
*** Initiating the SOSCF procedure ***
*** Re-Reading the Fockian ***
*** Removing any level shift ***
ITER Energy Delta-E Grad Rot Max-DP RMS-DP
0 -383.22271627 -383.2227162677 0.000398 0.000398 0.000593 0.000047
*** Restarting incremental Fock matrix formation ***
1 -383.22272274 -0.0000064770 0.000177 0.000191 0.000268 0.000021
2 -383.22272393 -0.0000011810 0.000063 0.000154 0.000140 0.000013
3 -383.22272409 -0.0000001657 0.000019 0.000042 0.000020 0.000001
4 -383.22272410 -0.0000000047 0.000010 0.000030 0.000016 0.000001
***Gradient check signals convergence***
***Rediagonalizing the Fockian in SOSCF/NRSCF***
*****************************************************
* SUCCESS *
* SCF CONVERGED AFTER 5 CYCLES *
*****************************************************
Total Energy : -383.22272410 Eh -10428.02047 eV
Last Energy change ... -1.7708e-09 Tolerance : 1.0000e-08
Last MAX-Density change ... 3.7487e-06 Tolerance : 1.0000e-07
**** THE GBW FILE WAS UPDATED (orca.gbw) ****
**** DENSITY FILE WAS UPDATED (orca.scfp.tmp) ****
**** ENERGY FILE WAS UPDATED (orca.en.tmp) ****
Total SCF time: 0 days 0 hours 0 min 29 sec
------------------------- --------------------
FINAL SINGLE POINT ENERGY -383.222724097876
------------------------- --------------------
------------------------------------------------------------------------------
ORCA SCF GRADIENT CALCULATION
------------------------------------------------------------------------------
Gradient of the Hartree-Fock SCF energy:
Hartree-Fock type ... RHF
Number of operators ... 1
Number of atoms ... 18
Basis set dimensions ... 106
Integral neglect threshold ... 2.5e-11
Integral primitive cutoff ... 2.5e-12
Nuclear repulsion gradient ... done
One Electron Gradient ... done
Pre-screening matrix ... done
Starting the two electron gradient:
Two electron gradient done
------------------
CARTESIAN GRADIENT
------------------
1 C : -0.000246790 0.000351719 -0.000001371
2 C : 0.000226127 0.000432441 0.000000849
3 C : -0.000413385 -0.000283441 -0.000000808
4 C : 0.000024468 0.000002305 0.000001218
5 C : -0.000423948 0.000289643 -0.000004048
6 C : 0.000233908 -0.000423526 0.000004729
7 C : -0.000237642 -0.000378759 -0.000002395
8 C : 0.000427593 0.000283314 0.000001265
9 C : -0.000048299 -0.000015806 -0.000000142
10 C : 0.000459220 -0.000248994 -0.000002667
11 H : 0.000061779 -0.000159463 0.000002227
12 H : -0.000060808 -0.000166476 -0.000002000
13 H : 0.000113794 0.000069823 -0.000001946
14 H : 0.000115593 -0.000075429 0.000006532
15 H : -0.000062115 0.000165299 -0.000001353
16 H : 0.000063078 0.000162103 -0.000005513
17 H : -0.000115283 -0.000074935 0.000004807
18 H : -0.000117291 0.000070180 0.000000615
Norm of the cartesian gradient ... 0.001451730
RMS gradient ... 0.000197555
MAX gradient ... 0.000459220
-------
TIMINGS
-------
Total SCF gradient time ... 17.631 sec
One electron gradient .... 0.283 sec ( 1.6%)
Prescreening matrices .... 0.090 sec ( 0.5%)
Two electron gradient .... 17.079 sec ( 96.9%)
------------------------------------------------------------------------------
ORCA GEOMETRY RELAXATION STEP
------------------------------------------------------------------------------
Reading the OPT-File .... done
Getting information on internals .... done
Copying old internal coords+grads .... done
Making the new internal coordinates .... (new redundants).... done
Validating the new internal coordinates .... (new redundants).... done
Calculating the B-matrix .... done
Calculating the G,G- and P matrices .... done
Transforming gradient to internals .... done
Projecting the internal gradient .... done
Number of atoms .... 18
Number of internal coordinates .... 93
Current Energy .... -383.222724098 Eh
Current gradient norm .... 0.001451730 Eh/bohr
Maximum allowed component of the step .... 0.300
Current trust radius .... 0.300
Updating the Hessian (BFGS) .... done
Forming the augmented Hessian .... done
Diagonalizing the augmented Hessian .... done
Last element of RFO vector .... 0.999995619
Lowest eigenvalues of augmented Hessian:
-0.000001956 0.020034786 0.020274388 0.020344596 0.023078294
Length of the computed step .... 0.002960180
The final length of the internal step .... 0.002960180
Converting the step to cartesian space:
Initial RMS(Int)= 0.0003069564
Transforming coordinates:
Iter 0: RMS(Cart)= 0.0005021216 RMS(Int)= 1.1284847608
Iter 1: RMS(Cart)= 0.0000002176 RMS(Int)= 0.0000001632
Iter 2: RMS(Cart)= 0.0000000002 RMS(Int)= 0.0000000001
done
Storing new coordinates .... done
.--------------------.
----------------------|Geometry convergence|---------------------
Item value Tolerance Converged
-----------------------------------------------------------------
Energy change -0.00001925 0.00000500 NO
RMS gradient 0.00008993 0.00010000 YES
MAX gradient 0.00031453 0.00030000 NO
RMS step 0.00030696 0.00200000 YES
MAX step 0.00086231 0.00400000 YES
....................................................
Max(Bonds) 0.0003 Max(Angles) 0.05
Max(Dihed) 0.01 Max(Improp) 0.00
-----------------------------------------------------------------
The step convergence is overachieved with
reasonable convergence on the gradient
Convergence will therefore be signaled now
***********************HURRAY********************
*** THE OPTIMIZATION HAS CONVERGED ***
*************************************************
---------------------------------------------------------------------------
Redundant Internal Coordinates
--- Optimized Parameters ---
(Angstroem and degrees)
Definition OldVal dE/dq Step FinalVal
----------------------------------------------------------------------------
1. B(C 1,C 0) 1.4156 -0.000030 -0.0000 1.4156
2. B(C 2,C 1) 1.3619 -0.000310 0.0002 1.3622
3. B(C 3,C 2) 1.4202 -0.000077 -0.0000 1.4202
4. B(C 4,C 3) 1.4202 -0.000081 -0.0000 1.4202
5. B(C 5,C 4) 1.3619 -0.000315 0.0003 1.3622
6. B(C 6,C 5) 1.4156 -0.000028 -0.0001 1.4156
7. B(C 7,C 6) 1.3619 -0.000299 0.0002 1.3622
8. B(C 8,C 7) 1.4202 -0.000070 -0.0000 1.4202
9. B(C 8,C 3) 1.4128 -0.000188 0.0003 1.4131
10. B(C 9,C 8) 1.4202 -0.000092 -0.0000 1.4202
11. B(C 9,C 0) 1.3620 -0.000293 0.0002 1.3622
12. B(H 10,C 0) 1.0731 0.000109 -0.0001 1.0730
13. B(H 11,C 1) 1.0731 0.000115 -0.0001 1.0730
14. B(H 12,C 2) 1.0742 0.000114 -0.0001 1.0741
15. B(H 13,C 4) 1.0742 0.000116 -0.0001 1.0741
16. B(H 14,C 5) 1.0731 0.000114 -0.0001 1.0730
17. B(H 15,C 6) 1.0731 0.000110 -0.0001 1.0730
18. B(H 16,C 7) 1.0742 0.000116 -0.0001 1.0741
19. B(H 17,C 9) 1.0742 0.000117 -0.0001 1.0741
20. A(C 9,C 0,H 10) 120.35 0.000151 -0.05 120.30
21. A(C 1,C 0,H 10) 119.41 -0.000116 0.05 119.46
22. A(C 1,C 0,C 9) 120.24 -0.000035 -0.00 120.23
23. A(C 0,C 1,C 2) 120.24 0.000001 -0.00 120.24
24. A(C 2,C 1,H 11) 120.35 0.000136 -0.05 120.30
25. A(C 0,C 1,H 11) 119.41 -0.000137 0.05 119.46
26. A(C 1,C 2,C 3) 120.81 0.000036 0.01 120.82
27. A(C 1,C 2,H 12) 120.44 0.000052 -0.03 120.41
28. A(C 3,C 2,H 12) 118.75 -0.000089 0.02 118.77
29. A(C 2,C 3,C 4) 122.11 0.000052 0.01 122.12
30. A(C 2,C 3,C 8) 118.95 -0.000027 -0.00 118.94
31. A(C 4,C 3,C 8) 118.95 -0.000025 -0.00 118.94
32. A(C 5,C 4,H 13) 120.44 0.000057 -0.03 120.41
33. A(C 3,C 4,H 13) 118.75 -0.000096 0.02 118.77
34. A(C 3,C 4,C 5) 120.81 0.000039 0.00 120.82
35. A(C 6,C 5,H 14) 119.41 -0.000136 0.05 119.46
36. A(C 4,C 5,H 14) 120.35 0.000139 -0.05 120.30
37. A(C 4,C 5,C 6) 120.24 -0.000003 -0.00 120.24
38. A(C 7,C 6,H 15) 120.35 0.000147 -0.05 120.30
39. A(C 5,C 6,H 15) 119.41 -0.000126 0.05 119.46
40. A(C 5,C 6,C 7) 120.24 -0.000022 -0.00 120.24
41. A(C 8,C 7,H 16) 118.75 -0.000097 0.02 118.77
42. A(C 6,C 7,H 16) 120.44 0.000055 -0.03 120.41
43. A(C 6,C 7,C 8) 120.81 0.000042 0.00 120.82
44. A(C 7,C 8,C 9) 122.11 0.000063 0.01 122.12
45. A(C 3,C 8,C 9) 118.94 -0.000032 -0.00 118.94
46. A(C 3,C 8,C 7) 118.94 -0.000031 -0.00 118.94
47. A(C 8,C 9,H 17) 118.75 -0.000099 0.02 118.77
48. A(C 0,C 9,H 17) 120.43 0.000042 -0.03 120.41
49. A(C 0,C 9,C 8) 120.82 0.000057 0.00 120.82
50. D(H 11,C 1,C 0,H 10) 0.01 0.000002 -0.00 0.00
51. D(C 2,C 1,C 0,C 9) 0.00 0.000001 -0.00 0.00
52. D(H 11,C 1,C 0,C 9) -180.00 0.000001 -0.00 -180.00
53. D(C 2,C 1,C 0,H 10) -180.00 0.000001 -0.00 -180.00
54. D(C 3,C 2,C 1,C 0) -0.00 -0.000000 0.00 -0.00
55. D(H 12,C 2,C 1,H 11) -0.00 0.000000 -0.00 -0.00
56. D(C 3,C 2,C 1,H 11) 180.00 -0.000001 0.00 180.00
57. D(H 12,C 2,C 1,C 0) -180.00 0.000000 -0.00 -180.00
58. D(C 8,C 3,C 2,H 12) 180.00 -0.000002 0.00 180.00
59. D(C 4,C 3,C 2,H 12) -0.00 -0.000001 0.00 -0.00
60. D(C 4,C 3,C 2,C 1) 180.00 -0.000000 0.00 180.00
61. D(C 8,C 3,C 2,C 1) -0.00 -0.000001 0.00 -0.00
62. D(H 13,C 4,C 3,C 2) -0.01 -0.000004 0.01 -0.01
63. D(C 5,C 4,C 3,C 8) -0.01 -0.000003 0.01 -0.00
64. D(C 5,C 4,C 3,C 2) 179.99 -0.000003 0.01 180.00
65. D(H 13,C 4,C 3,C 8) 179.99 -0.000004 0.01 180.00
66. D(H 14,C 5,C 4,H 13) 0.01 0.000003 -0.00 0.00
67. D(H 14,C 5,C 4,C 3) -180.00 0.000002 -0.00 -180.00
68. D(C 6,C 5,C 4,H 13) -179.99 0.000001 -0.00 -180.00
69. D(C 6,C 5,C 4,C 3) 0.00 0.000001 -0.00 0.00
70. D(H 15,C 6,C 5,H 14) 0.00 0.000001 -0.00 0.00
71. D(H 15,C 6,C 5,C 4) -179.99 0.000002 -0.00 -180.00
72. D(C 7,C 6,C 5,H 14) -180.00 0.000001 -0.00 -180.00
73. D(C 7,C 6,C 5,C 4) 0.01 0.000003 -0.01 -0.00
74. D(H 16,C 7,C 6,H 15) -0.01 -0.000003 0.00 -0.01
75. D(H 16,C 7,C 6,C 5) 179.99 -0.000003 0.01 180.00
76. D(C 8,C 7,C 6,H 15) 179.99 -0.000004 0.01 180.00
77. D(C 8,C 7,C 6,C 5) -0.01 -0.000004 0.01 0.00
78. D(C 9,C 8,C 3,C 2) 0.00 0.000001 -0.00 0.00
79. D(C 7,C 8,C 3,C 4) 0.00 0.000001 -0.00 0.00
80. D(C 7,C 8,C 3,C 2) -179.99 0.000002 -0.00 -180.00
81. D(C 9,C 8,C 7,H 16) 0.01 0.000001 -0.00 0.00
82. D(C 9,C 8,C 7,C 6) -179.99 0.000003 -0.01 -180.00
83. D(C 3,C 8,C 7,H 16) -180.00 0.000001 -0.00 -180.00
84. D(C 3,C 8,C 7,C 6) 0.00 0.000002 -0.01 -0.00
85. D(C 9,C 8,C 3,C 4) -180.00 0.000001 -0.00 -180.00
86. D(H 17,C 9,C 8,C 7) -0.01 -0.000001 0.00 -0.00
87. D(C 0,C 9,C 8,C 7) 179.99 -0.000001 0.00 180.00
88. D(C 0,C 9,C 8,C 3) -0.00 -0.000001 0.00 -0.00
89. D(H 17,C 9,C 0,H 10) -0.00 -0.000001 0.00 -0.00
90. D(H 17,C 9,C 0,C 1) 180.00 -0.000000 0.00 180.00
91. D(H 17,C 9,C 8,C 3) 180.00 -0.000001 0.00 180.00
92. D(C 8,C 9,C 0,H 10) 180.00 -0.000001 0.00 180.00
93. D(C 8,C 9,C 0,C 1) -0.00 -0.000001 0.00 0.00
----------------------------------------------------------------------------
*******************************************************
*** FINAL ENERGY EVALUATION AT THE STATIONARY POINT ***
*** (AFTER 4 CYCLES) ***
*******************************************************
---------------------------------
CARTESIAN COORDINATES (ANGSTROEM)
---------------------------------
C -0.051758 -0.021974 -0.036755
C 1.363805 -0.020980 -0.037802
C 2.049045 1.156301 -0.037669
C 1.360952 2.398653 -0.036503
C 2.047390 3.641918 -0.036362
C 1.360573 4.818278 -0.035293
C -0.054989 4.817349 -0.034265
C -0.740204 3.640045 -0.034374
C -0.052103 2.397700 -0.035479
C -0.738510 1.154439 -0.035621
H -0.578876 -0.956605 -0.036852
H 1.892170 -0.954919 -0.038715
H 3.123106 1.160238 -0.038471
H 3.121457 3.639406 -0.037071
H 1.887668 5.752933 -0.035187
H -0.583333 5.751291 -0.033457
H -1.814269 3.636093 -0.033564
H -1.812583 1.156945 -0.034830
----------------------------
CARTESIAN COORDINATES (A.U.)
----------------------------
NO LB ZA FRAG MASS X Y Z
0 C 6.0000 0 12.011 -0.097808587366012 -0.041525614253398 -0.069457457688540
1 C 6.0000 0 12.011 2.577218085771947 -0.039646514820953 -0.071434675601637
2 C 6.0000 0 12.011 3.872133279582767 2.185092203262714 -0.071183826914644
3 C 6.0000 0 12.011 2.571827500871817 4.532797680644739 -0.068980566205794
4 C 6.0000 0 12.011 3.869007161483661 6.882227230101384 -0.068714970388639
5 C 6.0000 0 12.011 2.571110660629270 9.105226205078942 -0.066693753684580
6 C 6.0000 0 12.011 -0.103914805453304 9.103469379884936 -0.064751984013582
7 C 6.0000 0 12.011 -1.398783382343948 6.878688135605014 -0.064956610437512
8 C 6.0000 0 12.011 -0.098460029094429 4.530997026388878 -0.067046298322635
9 C 6.0000 0 12.011 -1.395582400998665 2.181573383428006 -0.067314806789926
10 H 1.0000 0 1.008 -1.093917854675867 -1.807720719900320 -0.069639815922130
11 H 1.0000 0 1.008 3.575683466556944 -1.804535173509403 -0.073160468241592
12 H 1.0000 0 1.008 5.901815125138685 2.192532166106772 -0.072700342028320
13 H 1.0000 0 1.008 5.898698648625760 6.877479686261953 -0.070053154297940
14 H 1.0000 0 1.008 3.567174734295732 10.871466983046263 -0.066493637588352
15 H 1.0000 0 1.008 -1.102339932631247 10.868364388411189 -0.063224244387263
16 H 1.0000 0 1.008 -3.428470979737443 6.871219971011075 -0.063427029755755
17 H 1.0000 0 1.008 -3.425286107084926 2.186309476105605 -0.065819118568289
--------------------------------
INTERNAL COORDINATES (ANGSTROEM)
--------------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 1.415564 0.000 0.000
C 2 1 0 1.362184 120.242 0.000
C 3 2 1 1.420180 120.818 0.000
C 4 3 2 1.420177 122.115 180.001
C 5 4 3 1.362183 120.817 179.997
C 6 5 4 1.415563 120.241 0.000
C 7 6 5 1.362191 120.238 0.000
C 4 3 2 1.413056 118.942 0.000
C 1 2 3 1.362196 120.235 0.000
H 1 2 3 1.073027 119.463 180.001
H 2 1 3 1.073039 119.458 180.001
H 3 2 1 1.074069 120.412 180.001
H 5 4 3 1.074070 118.770 0.000
H 6 5 4 1.073036 120.301 180.000
H 7 6 5 1.073031 119.460 180.002
H 8 7 6 1.074072 120.411 179.998
H 10 1 2 1.074076 120.409 180.000
---------------------------
INTERNAL COORDINATES (A.U.)
---------------------------
C 0 0 0 0.000000 0.000 0.000
C 1 0 0 2.675028 0.000 0.000
C 2 1 0 2.574154 120.242 0.000
C 3 2 1 2.683751 120.818 0.000
C 4 3 2 2.683746 122.115 180.001
C 5 4 3 2.574153 120.817 179.997
C 6 5 4 2.675027 120.241 0.000
C 7 6 5 2.574167 120.238 0.000
C 4 3 2 2.670289 118.942 0.000
C 1 2 3 2.574178 120.235 0.000
H 1 2 3 2.027728 119.463 180.001
H 2 1 3 2.027750 119.458 180.001
H 3 2 1 2.029696 120.412 180.001
H 5 4 3 2.029697 118.770 0.000
H 6 5 4 2.027745 120.301 180.000
H 7 6 5 2.027735 119.460 180.002
H 8 7 6 2.029702 120.411 179.998
H 10 1 2 2.029710 120.409 180.000
---------------------
BASIS SET INFORMATION
---------------------
There are 2 groups of distinct atoms
Group 1 Type C : 10s4p contracted to 3s2p pattern {631/31}
Group 2 Type H : 4s contracted to 2s pattern {31}
Atom 0C basis set group => 1
Atom 1C basis set group => 1
Atom 2C basis set group => 1
Atom 3C basis set group => 1
Atom 4C basis set group => 1
Atom 5C basis set group => 1
Atom 6C basis set group => 1
Atom 7C basis set group => 1
Atom 8C basis set group => 1
Atom 9C basis set group => 1
Atom 10H basis set group => 2
Atom 11H basis set group => 2
Atom 12H basis set group => 2
Atom 13H basis set group => 2
Atom 14H basis set group => 2
Atom 15H basis set group => 2
Atom 16H basis set group => 2
Atom 17H basis set group => 2
------------------------------------------------------------------------------
ORCA GTO INTEGRAL CALCULATION
------------------------------------------------------------------------------
BASIS SET STATISTICS AND STARTUP INFO
# of primitive gaussian shells ... 172
# of primitive gaussian functions ... 252
# of contracted shell ... 66
# of contracted basis functions ... 106
Highest angular momentum ... 1
Maximum contraction depth ... 6
Integral package used ... LIBINT
Integral threshhold Thresh ... 2.500e-11
Primitive cut-off TCut ... 2.500e-12
INTEGRAL EVALUATION
One electron integrals ... done
Pre-screening matrix ... done
Shell pair data ... done ( 0.003 sec)
-------------------------------------------------------------------------------
ORCA SCF
-------------------------------------------------------------------------------
------------
SCF SETTINGS
------------
Hamiltonian:
Ab initio Hamiltonian Method .... Hartree-Fock(GTOs)
General Settings:
Integral files IntName .... orca
Hartree-Fock type HFTyp .... RHF
Total Charge Charge .... 0
Multiplicity Mult .... 1
Number of Electrons NEL .... 68
Basis Dimension Dim .... 106
Nuclear Repulsion ENuc .... 460.0270955572 Eh
Convergence Acceleration:
DIIS CNVDIIS .... on
Start iteration DIISMaxIt .... 12
Startup error DIISStart .... 0.200000
# of expansion vecs DIISMaxEq .... 5
Bias factor DIISBfac .... 1.050
Max. coefficient DIISMaxC .... 10.000
Newton-Raphson CNVNR .... off
SOSCF CNVSOSCF .... on
Start iteration SOSCFMaxIt .... 150
Startup grad/error SOSCFStart .... 0.003300
Level Shifting CNVShift .... on
Level shift para. LevelShift .... 0.2500
Turn off err/grad. ShiftErr .... 0.0010
Zerner damping CNVZerner .... off
Static damping CNVDamp .... on
Fraction old density DampFac .... 0.7000
Max. Damping (<1) DampMax .... 0.9800
Min. Damping (>=0) DampMin .... 0.0000
Turn off err/grad. DampErr .... 0.1000
Fernandez-Rico CNVRico .... off
SCF Procedure:
Maximum # iterations MaxIter .... 125
SCF integral mode SCFMode .... Direct
Integral package .... LIBINT
Reset frequeny DirectResetFreq .... 20
Integral Threshold Thresh .... 2.500e-11 Eh
Primitive CutOff TCut .... 2.500e-12 Eh
Convergence Tolerance:
Convergence Check Mode ConvCheckMode .... Total+1el-Energy
Energy Change TolE .... 1.000e-08 Eh
1-El. energy change .... 1.000e-05 Eh
Orbital Gradient TolG .... 1.000e-05
Orbital Rotation angle TolX .... 1.000e-05
DIIS Error TolErr .... 5.000e-07
Diagonalization of the overlap matrix:
Smallest eigenvalue ... 3.765e-04
Time for diagonalization ... 0.004 sec
Threshold for overlap eigenvalues ... 1.000e-08
Number of eigenvalues below threshold ... 0
Time for construction of square roots ... 0.002 sec
Total time needed ... 0.006 sec
---------------------
INITIAL GUESS: MOREAD
---------------------
Guess MOs are being read from file: orca.gbw
Input Geometry matches current geometry (good)
Input basis set matches current basis set (good)
MOs were renormalized
MOs were reorthogonalized (Schmidt)
------------------
INITIAL GUESS DONE ( 0.0 sec)
------------------
--------------
SCF ITERATIONS
--------------
ITER Energy Delta-E Max-DP RMS-DP [F,P] Damp
*** Starting incremental Fock matrix formation ***
*** Initiating the SOSCF procedure ***
*** Re-Reading the Fockian ***
*** Removing any level shift ***
ITER Energy Delta-E Grad Rot Max-DP RMS-DP
0 -383.22272495 -383.2227249517 0.000073 0.000073 0.000109 0.000010
*** Restarting incremental Fock matrix formation ***
1 -383.22272523 -0.0000002828 0.000029 0.000055 0.000053 0.000004
2 -383.22272529 -0.0000000526 0.000015 0.000047 0.000025 0.000003
3 -383.22272530 -0.0000000095 0.000006 0.000013 0.000007 0.000000
4 -383.22272530 -0.0000000011 0.000003 0.000007 0.000003 0.000000
***Gradient check signals convergence***
***Rediagonalizing the Fockian in SOSCF/NRSCF***
*****************************************************
* SUCCESS *
* SCF CONVERGED AFTER 5 CYCLES *
*****************************************************
----------------
TOTAL SCF ENERGY
----------------
Total Energy : -383.22272530 Eh -10428.02051 eV
Components:
Nuclear Repulsion : 460.02709556 Eh 12517.97367 eV
Electronic Energy : -843.24982085 Eh -22945.99418 eV
One Electron Energy: -1429.01997970 Eh -38885.61055 eV
Two Electron Energy: 585.77015885 Eh 15939.61638 eV
Virial components:
Potential Energy : -766.91689377 Eh -20868.86963 eV
Kinetic Energy : 383.69416848 Eh 10440.84913 eV
Virial Ratio : 1.99877130
---------------
SCF CONVERGENCE
---------------
Last Energy change ... 3.2355e-10 Tolerance : 1.0000e-08
Last MAX-Density change ... 6.8461e-07 Tolerance : 1.0000e-07
Last RMS-Density change ... 6.6836e-08 Tolerance : 5.0000e-09
Last Orbital Gradient ... 3.1870e-07 Tolerance : 1.0000e-05
Last Orbital Rotation ... 4.1292e-07 Tolerance : 1.0000e-05
**** THE GBW FILE WAS UPDATED (orca.gbw) ****
**** DENSITY FILE WAS UPDATED (orca.scfp.tmp) ****
**** ENERGY FILE WAS UPDATED (orca.en.tmp) ****
----------------
ORBITAL ENERGIES
----------------
NO OCC E(Eh) E(eV)
0 2.0000 -11.245805 -306.0139
1 2.0000 -11.244744 -305.9850
2 2.0000 -11.237119 -305.7775
3 2.0000 -11.237084 -305.7766
4 2.0000 -11.236859 -305.7705
5 2.0000 -11.236791 -305.7686
6 2.0000 -11.235719 -305.7395
7 2.0000 -11.235691 -305.7387
8 2.0000 -11.234979 -305.7193
9 2.0000 -11.234965 -305.7190
10 2.0000 -1.182174 -32.1686
11 2.0000 -1.115516 -30.3547
12 2.0000 -1.052496 -28.6399
13 2.0000 -1.011010 -27.5110
14 2.0000 -0.986654 -26.8482
15 2.0000 -0.853601 -23.2277
16 2.0000 -0.837889 -22.8001
17 2.0000 -0.815433 -22.1891
18 2.0000 -0.705109 -19.1870
19 2.0000 -0.704583 -19.1727
20 2.0000 -0.680670 -18.5220
21 2.0000 -0.622059 -16.9271
22 2.0000 -0.613450 -16.6928
23 2.0000 -0.585182 -15.9236
24 2.0000 -0.585134 -15.9223
25 2.0000 -0.564469 -15.3600
26 2.0000 -0.534287 -14.5387
27 2.0000 -0.519868 -14.1463
28 2.0000 -0.482877 -13.1397
29 2.0000 -0.470790 -12.8108
30 2.0000 -0.447454 -12.1759
31 2.0000 -0.383405 -10.4330
32 2.0000 -0.318172 -8.6579
33 2.0000 -0.287780 -7.8309
34 0.0000 0.100061 2.7228
35 0.0000 0.132478 3.6049
36 0.0000 0.191045 5.1986
37 0.0000 0.239286 6.5113
38 0.0000 0.260699 7.0940
39 0.0000 0.265143 7.2149
40 0.0000 0.288299 7.8450
41 0.0000 0.312104 8.4928
42 0.0000 0.316351 8.6084
43 0.0000 0.325076 8.8458
44 0.0000 0.338925 9.2226
45 0.0000 0.360395 9.8069
46 0.0000 0.416259 11.3270
47 0.0000 0.416844 11.3429
48 0.0000 0.468271 12.7423
49 0.0000 0.490268 13.3409
50 0.0000 0.499135 13.5822
51 0.0000 0.503688 13.7060
52 0.0000 0.516577 14.0568
53 0.0000 0.546220 14.8634
54 0.0000 0.697831 18.9890
55 0.0000 0.732970 19.9451
56 0.0000 0.739531 20.1237
57 0.0000 0.750749 20.4289
58 0.0000 0.761619 20.7247
59 0.0000 0.774746 21.0819
60 0.0000 0.778919 21.1955
61 0.0000 0.788282 21.4502
62 0.0000 0.811585 22.0844
63 0.0000 0.817251 22.2385
64 0.0000 0.829457 22.5707
65 0.0000 0.859497 23.3881
66 0.0000 0.865523 23.5521
67 0.0000 0.870225 23.6800
68 0.0000 0.884116 24.0580
69 0.0000 0.884677 24.0733
70 0.0000 0.902987 24.5715
71 0.0000 0.909176 24.7399
72 0.0000 0.912796 24.8384
73 0.0000 0.922725 25.1086
74 0.0000 0.943138 25.6641
75 0.0000 0.943970 25.6867
76 0.0000 1.010185 27.4885
77 0.0000 1.081938 29.4410
78 0.0000 1.122330 30.5401
79 0.0000 1.132257 30.8103
80 0.0000 1.138328 30.9755
81 0.0000 1.139049 30.9951
82 0.0000 1.162339 31.6289
83 0.0000 1.187740 32.3200
84 0.0000 1.190081 32.3838
85 0.0000 1.227049 33.3897
86 0.0000 1.227969 33.4147
87 0.0000 1.249736 34.0070
88 0.0000 1.276921 34.7468
89 0.0000 1.309249 35.6265
90 0.0000 1.310819 35.6692
91 0.0000 1.349103 36.7110
92 0.0000 1.356951 36.9245
93 0.0000 1.367311 37.2064
94 0.0000 1.392599 37.8946
95 0.0000 1.439614 39.1739
96 0.0000 1.501010 40.8446
97 0.0000 1.513174 41.1756
98 0.0000 1.573588 42.8195
99 0.0000 1.631488 44.3950
100 0.0000 1.739820 47.3429
101 0.0000 1.770121 48.1674
102 0.0000 1.793079 48.7921
103 0.0000 1.840400 50.0798
104 0.0000 2.207664 60.0736
105 0.0000 2.209546 60.1248
********************************
* MULLIKEN POPULATION ANALYSIS *
********************************
-----------------------
MULLIKEN ATOMIC CHARGES
-----------------------
0 C : -0.207180
1 C : -0.207219
2 C : -0.163595
3 C : -0.074353
4 C : -0.163596
5 C : -0.207210
6 C : -0.207198
7 C : -0.163601
8 C : -0.074320
9 C : -0.163639
10 H : 0.200129
11 H : 0.200106
12 H : 0.207865
13 H : 0.207867
14 H : 0.200110
15 H : 0.200120
16 H : 0.207863
17 H : 0.207853
Sum of atomic charges: -0.0000000
--------------------------------
MULLIKEN REDUCED ORBITAL CHARGES
--------------------------------
0 C s : 3.179235 s : 3.179235
pz : 1.003762 p : 3.027945
px : 0.951072
py : 1.073111
1 C s : 3.179267 s : 3.179267
pz : 1.003748 p : 3.027952
px : 0.951317
py : 1.072887
2 C s : 3.127751 s : 3.127751
pz : 1.003029 p : 3.035843
px : 1.117892
py : 0.914922
3 C s : 3.127432 s : 3.127432
pz : 0.986444 p : 2.946922
px : 0.913614
py : 1.046864
4 C s : 3.127752 s : 3.127752
pz : 1.003022 p : 3.035843
px : 1.117968
py : 0.914853
5 C s : 3.179262 s : 3.179262
pz : 1.003749 p : 3.027948
px : 0.951078
py : 1.073121
6 C s : 3.179249 s : 3.179249
pz : 1.003762 p : 3.027950
px : 0.951301
py : 1.072887
7 C s : 3.127762 s : 3.127762
pz : 1.003007 p : 3.035839
px : 1.117902
py : 0.914929
8 C s : 3.127414 s : 3.127414
pz : 0.986469 p : 2.946906
px : 0.913609
py : 1.046827
9 C s : 3.127782 s : 3.127782
pz : 1.003008 p : 3.035856
px : 1.117979
py : 0.914869
10 H s : 0.799871 s : 0.799871
11 H s : 0.799894 s : 0.799894
12 H s : 0.792135 s : 0.792135
13 H s : 0.792133 s : 0.792133
14 H s : 0.799890 s : 0.799890
15 H s : 0.799880 s : 0.799880
16 H s : 0.792137 s : 0.792137
17 H s : 0.792147 s : 0.792147
*******************************
* LOEWDIN POPULATION ANALYSIS *
*******************************
----------------------
LOEWDIN ATOMIC CHARGES
----------------------
0 C : -0.123353
1 C : -0.123345
2 C : -0.110816
3 C : -0.023221
4 C : -0.110812
5 C : -0.123346
6 C : -0.123353
7 C : -0.110801
8 C : -0.023236
9 C : -0.110804
10 H : 0.123232
11 H : 0.123223
12 H : 0.122546
13 H : 0.122546
14 H : 0.123225
15 H : 0.123229
16 H : 0.122545
17 H : 0.122541
-------------------------------
LOEWDIN REDUCED ORBITAL CHARGES
-------------------------------
0 C s : 2.933862 s : 2.933862
pz : 1.003568 p : 3.189491
px : 1.080682
py : 1.105242
1 C s : 2.933861 s : 2.933861
pz : 1.003554 p : 3.189484
px : 1.080706
py : 1.105224
2 C s : 2.930545 s : 2.930545
pz : 1.004635 p : 3.180271
px : 1.103146
py : 1.072491
3 C s : 2.890334 s : 2.890334
pz : 0.983621 p : 3.132887
px : 1.075934
py : 1.073332
4 C s : 2.930545 s : 2.930545
pz : 1.004629 p : 3.180267
px : 1.103180
py : 1.072458
5 C s : 2.933861 s : 2.933861
pz : 1.003555 p : 3.189485
px : 1.080686
py : 1.105244
6 C s : 2.933861 s : 2.933861
pz : 1.003567 p : 3.189493
px : 1.080701
py : 1.105224
7 C s : 2.930548 s : 2.930548
pz : 1.004615 p : 3.180253
px : 1.103145
py : 1.072493
8 C s : 2.890329 s : 2.890329
pz : 0.983643 p : 3.132907
px : 1.075932
py : 1.073332
9 C s : 2.930547 s : 2.930547
pz : 1.004614 p : 3.180257
px : 1.103177
py : 1.072466
10 H s : 0.876768 s : 0.876768
11 H s : 0.876777 s : 0.876777
12 H s : 0.877454 s : 0.877454
13 H s : 0.877454 s : 0.877454
14 H s : 0.876775 s : 0.876775
15 H s : 0.876771 s : 0.876771
16 H s : 0.877455 s : 0.877455
17 H s : 0.877459 s : 0.877459
*****************************
* MAYER POPULATION ANALYSIS *
*****************************
NA - Mulliken gross atomic population
ZA - Total nuclear charge
QA - Mulliken gross atomic charge
VA - Mayer's total valence
BVA - Mayer's bonded valence
FA - Mayer's free valence
ATOM NA ZA QA VA BVA FA
0 C 6.2072 6.0000 -0.2072 3.8691 3.8691 0.0000
1 C 6.2072 6.0000 -0.2072 3.8691 3.8691 -0.0000
2 C 6.1636 6.0000 -0.1636 3.8874 3.8874 0.0000
3 C 6.0744 6.0000 -0.0744 3.8867 3.8867 -0.0000
4 C 6.1636 6.0000 -0.1636 3.8874 3.8874 -0.0000
5 C 6.2072 6.0000 -0.2072 3.8691 3.8691 0.0000
6 C 6.2072 6.0000 -0.2072 3.8691 3.8691 -0.0000
7 C 6.1636 6.0000 -0.1636 3.8874 3.8874 -0.0000
8 C 6.0743 6.0000 -0.0743 3.8867 3.8867 -0.0000
9 C 6.1636 6.0000 -0.1636 3.8874 3.8874 0.0000
10 H 0.7999 1.0000 0.2001 0.9334 0.9334 0.0000
11 H 0.7999 1.0000 0.2001 0.9334 0.9334 -0.0000
12 H 0.7921 1.0000 0.2079 0.9285 0.9285 -0.0000
13 H 0.7921 1.0000 0.2079 0.9285 0.9285 -0.0000
14 H 0.7999 1.0000 0.2001 0.9334 0.9334 0.0000
15 H 0.7999 1.0000 0.2001 0.9334 0.9334 -0.0000
16 H 0.7921 1.0000 0.2079 0.9285 0.9285 -0.0000
17 H 0.7921 1.0000 0.2079 0.9285 0.9285 0.0000
Mayer bond orders larger than 0.1
B( 0-C , 1-C ) : 1.2802 B( 0-C , 9-C ) : 1.6169 B( 0-C , 10-H ) : 0.9411
B( 1-C , 2-C ) : 1.6169 B( 1-C , 11-H ) : 0.9411 B( 2-C , 3-C ) : 1.2592
B( 2-C , 12-H ) : 0.9353 B( 3-C , 4-C ) : 1.2592 B( 3-C , 8-C ) : 1.3498
B( 4-C , 5-C ) : 1.6169 B( 4-C , 13-H ) : 0.9353 B( 5-C , 6-C ) : 1.2801
B( 5-C , 14-H ) : 0.9411 B( 6-C , 7-C ) : 1.6169 B( 6-C , 15-H ) : 0.9411
B( 7-C , 8-C ) : 1.2592 B( 7-C , 16-H ) : 0.9353 B( 8-C , 9-C ) : 1.2592
B( 9-C , 17-H ) : 0.9353
-------
TIMINGS
-------
Total SCF time: 0 days 0 hours 0 min 28 sec
Total time .... 28.252 sec
Sum of individual times .... 28.239 sec (100.0%)
Fock matrix formation .... 28.193 sec ( 99.8%)
Diagonalization .... 0.005 sec ( 0.0%)
Density matrix formation .... 0.002 sec ( 0.0%)
Population analysis .... 0.009 sec ( 0.0%)
Initial guess .... 0.012 sec ( 0.0%)
Orbital Transformation .... 0.000 sec ( 0.0%)
Orbital Orthonormalization .... 0.010 sec ( 0.0%)
DIIS solution .... 0.001 sec ( 0.0%)
SOSCF solution .... 0.017 sec ( 0.1%)
------------------------- --------------------
FINAL SINGLE POINT ENERGY -383.222725297383
------------------------- --------------------
*** OPTIMIZATION RUN DONE ***
***************************************
* ORCA property calculations *
***************************************
---------------------
Active property flags
---------------------
(+) Dipole Moment
------------------------------------------------------------------------------
ORCA ELECTRIC PROPERTIES CALCULATION
------------------------------------------------------------------------------
Dipole Moment Calculation ... on
Quadrupole Moment Calculation ... off
Polarizability Calculation ... off
GBWName ... orca.gbw
Electron density file ... orca.scfp.tmp
-------------
DIPOLE MOMENT
-------------
X Y Z
Electronic contribution: -0.00000 0.00001 0.00004
Nuclear contribution : -0.00002 -0.00000 -0.00004
-----------------------------------------
Total Dipole Moment : -0.00002 0.00001 0.00000
-----------------------------------------
Magnitude (a.u.) : 0.00002
Magnitude (Debye) : 0.00006
Timings for individual modules:
Sum of individual times ... 267.622 sec (= 4.460 min)
GTO integral calculation ... 2.424 sec (= 0.040 min) 0.9 %
SCF iterations ... 190.192 sec (= 3.170 min) 71.1 %
SCF Gradient evaluation ... 72.367 sec (= 1.206 min) 27.0 %
Geometry relaxation ... 2.639 sec (= 0.044 min) 1.0 %
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 4 minutes 28 seconds 233 msec
На основе полученных координат составим новые входные файлы и рассчитаем энергию (FINAL SINGLE POINT ENERGY) методом Хартри-Фока и используя теорию функционала плотности (заголовок !DFT RHF 6-31G):
In [11]:
%%bash
/srv/databases/orca/orca orca.inp > orca_HF.txt
In [12]:
%%bash
/srv/databases/orca/orca orca.inp > orca_DFT.txt
Algorithm |
E Naphthalene |
Hartree-Fock |
-383.223 |
DFT |
-382.253 |
Энергии, полученные двумя разными методами, различаются на 0,97 Hartree, или на 608.68 kcal/mol. К сожалению, для азулена получить значения энергии не получилось, а на основе этих данных нельзя заключить, какой метод лучше.